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: GOstats

https://packages.ecosyste.ms/registries/bioconductor.org/packages/GOstats

Tools for manipulating GO and microarrays
2 versions
Latest release: about 1 year ago
23 dependent packages
478,137 downloads total

Papers Mentioning GOstats 368

10.1038/s41598-018-21506-7
CXCL12/CXCR4-Mediated Procollagen Secretion Is Coupled To Cullin-RING Ubiquitin Ligase Activation
Cited by: 13
Author(s): Susan Patalano, Jose Antonio Rodriguez-Nieves, Cory Colaneri, Justin Cotellessa, Diego Almanza, Alisa Zhilin-Roth, Todd Riley, Jill A. Macoska
Software Mentions: 3
Published: over 6 years ago
10.1186/s12864-015-2100-5
Investigating inter-chromosomal regulatory relationships through a comprehensive meta-analysis of matched copy number and transcriptomics data sets
Cited by: 5
Author(s): Richard Newton, Lorenz Wernisch
Software Mentions: 3
Published: about 9 years ago
10.1186/s13059-019-1713-4
Single-cell transcriptomics unveils gene regulatory network plasticity
Cited by: 161
Author(s): Giovanni Iacono, Ramón Massoni-Badosa, Holger Heyn
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-020-57723-2
The FGF, TGFβ and WNT axis Modulate Self-renewal of Human SIX2+ Urine Derived Renal Progenitor Cells
Cited by: 28
Author(s): Shaifur Rahman, Wasco Wruck, Lucas‐Sebastian Spitzhorn, Lisa Nguyen, Martina Bohndorf, Soraia Martins, Fatima Asar, Audrey Ncube, Lars Erichsen, Nina Graffmann, James Adjaye
Software Mentions: 3
Published: almost 5 years ago
10.1186/1756-0500-4-160
The dynamics of E1A in regulating networks and canonical pathways in quiescent cells
Cited by: 6
Author(s): Jean-Eudes Dazard, Keman Zhang, Jingfeng Sha, Yasin Omar, Linda Cai, Chien Ngoc Nguyen, Mrinal K. Ghosh, Jennifer Bongorno, Marian L. Harter
Software Mentions: 3
Published: over 13 years ago
10.1186/1471-2164-13-623
High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome
Cited by: 46
Author(s): Danni Yu, John Danku, Ivan Baxter, Sungjin Kim, Olena K. Vatamaniuk, Olga Vitek, Mourad Ouzzani, David E. Salt
Software Mentions: 3
Published: about 12 years ago
10.1186/1471-2105-8-90
Importance of data structure in comparing two dimension reduction methods for classification of microarray gene expression data
Cited by: 10
Author(s): Caroline Truntzer, Catherine Mercier, Jacques Estève, Christian Gautier, Pascal Roy
Software Mentions: 3
Published: over 17 years ago
10.1038/srep37622
HMGA1P7-pseudogene regulates H19 and Igf2 expression by a competitive endogenous RNA mechanism
Cited by: 33
Author(s): Marco De Martino, Floriana Forzati, Marianna Marfella, Simona Pellecchia, Claudio Arra, Luigi Terracciano, Alfredo Fusco, Francesco Esposito
Software Mentions: 3
Published: almost 8 years ago
10.1186/2040-2392-5-38
Integrative proteomic analysis of the NMDA NR1 knockdown mouse model reveals effects on central and peripheral pathways associated with schizophrenia and autism spectrum disorders
Cited by: 31
Author(s): Hendrik Wesseling, Paul C. Guest, Chi-Ming Lee, Erik H. F. Wong, Hassan Rahmoune, Sabine Bahn
Software Mentions: 3
Published: over 10 years ago
10.1186/1471-2334-10-176
Tracking the transcriptional host response from the acute to the regenerative phase of experimental pneumococcal meningitis
Cited by: 16
Author(s): Matthias Wittwer, Denis Grandgirard, Janine Rohrbach, Stephen L. Leib
Software Mentions: 3
Published: over 14 years ago
10.1186/2043-9113-1-15
Functional similarity analysis of human virus-encoded miRNAs
Cited by: 14
Author(s): Guangchuang Yu, Qing-Yu He
Software Mentions: 3
Published: almost 14 years ago
10.18632/oncotarget.23537
Upregulation of cell cycle genes in head and neck cancer patients may be antagonized by erufosine’s down regulation of cell cycle processes in OSCC cells
Cited by: 13
Author(s): Shariq Ansari, Ashwini Kumar Sharma, Michael Zepp, Elizabet Ivanova, Frank Bergmann, Rainer König, Martin R. Berger
Software Mentions: 3
Published: almost 7 years ago
10.3390/e23010002
Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data
Cited by: 29
Author(s): Malik Yousef, Abhishek Kumar, Burcu Bakır-Güngör
Software Mentions: 3
Published: almost 4 years ago
10.7717/peerj.8456
Key genes and co-expression modules involved in asthma pathogenesis
Cited by: 12
Author(s): Yuyi Huang, Hui Liu, Li Zuo, Ailin Tao
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12864-016-3433-4
Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model
Cited by: 24
Author(s): Kathy Schall, Matthew E. Thornton, Mubina Isani, Kathleen A. Holoyda, Xiaogang Hou, Ching‐Ling Lien, Brendan H. Grubbs, Tracy C. Grikscheit
Software Mentions: 3
Published: almost 8 years ago
10.1098/rsos.170910
Gene expression differs in susceptible and resistant amphibians exposed to <i>Batrachochytrium dendrobatidis</i>
Cited by: 32
Author(s): Evan A. Eskew, Barbara C. Shock, Elise E B LaDouceur, Kevin Keel, Michael R. Miller, Janet E. Foley, Brian D. Todd
Software Mentions: 3
Published: almost 7 years ago
10.1038/s41598-020-67588-0
Glomerular endothelial cell heterogeneity in Alport syndrome
Cited by: 8
Author(s): Hasmik Soloyan, Matthew E. Thornton, Valentina Villani, Patrick Khatchadourian, Paolo Cravedi, Andrea Angeletti, Brendan H. Grubbs, Roger De Filippo, Laura Perin, Sargis Sedrakyan
Software Mentions: 3
Published: over 4 years ago
10.1186/s12977-016-0248-y
TLR8 regulation of LILRA3 in monocytes is abrogated in human immunodeficiency virus infection and correlates to CD4 counts and virus loads
Cited by: 8
Author(s): Hui Zhi Low, Gerrit Ahrenstorf, Claudia Pommerenke, Nadine Habermann, Klaus Schughart, David Ordóñez, Renata Stripecke, Esther Wilk, Torsten Witte
Software Mentions: 3
Published: over 8 years ago
10.1186/s13007-017-0159-5
Medical Subject Heading (MeSH) annotations illuminate maize genetics and evolution
Cited by: 7
Author(s): Timothy Beissinger, Gota Morota
Software Mentions: 3
Published: over 7 years ago
10.3389/fnagi.2017.00064
Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease
Cited by: 9
Author(s): Francisco Altimiras, Barbara Uszczyńska-Ratajczak, Francisco Câmara, Anna Vlasova, Emilio Palumbo, Stephen Newhouse, Robert M. J. Deacon, Leandro A. E. Farias, Michael Hurley, David E. Loyola, Rodrigo A. Vásquez, Richard Dobson, Roderic Guigó, Patricia Cogram
Software Mentions: 3
Published: over 7 years ago
10.1186/1471-2105-14-284
DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures
Cited by: 30
Author(s): Gaston K. Mazandu, Nicola Mulder
Software Mentions: 3
Published: about 11 years ago
10.1155/2008/619832
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics
Cited by: 1,633
Author(s): Ana Conesa, Stefan Götz
Software Mentions: 3
Published: over 16 years ago
10.1186/s12866-015-0532-3
Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A
Cited by: 45
Author(s): Jennifer M. H. Geddes, Daniel Croll, Mélissa Caza, Nikolay Stoynov, Leonard J. Foster, James W. Kronstad
Software Mentions: 2
Published: about 9 years ago
10.1186/s12864-020-6666-1
Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas
Cited by: 2
Author(s): Fatemeh Maghuly, Tamás Deák, Klemens Vierlinger, Stephan Pabinger, Hakim Tafer, Margit Laimer
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2164-12-130
In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis
Cited by: 88
Author(s): Bart Buitenhuis, Christine M. Røntved, Stefan McKinnon Edwards, K.L. Ingvartsen, Peter Sørensen
Software Mentions: 2
Published: over 13 years ago
10.1186/1471-2164-14-716
Global regulatory architecture of human, mouse and rat tissue transcriptomes
Cited by: 19
Author(s): Ajay Prasad, Suchitra Suresh Kumar, Christophe Dessimoz, Stefan Bleuler, Oliver Laule, Tomás Hrúz, Wilhelm Gruissem, Philip Zimmermann
Software Mentions: 2
Published: about 11 years ago
10.1186/1471-2164-11-711
Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq
Cited by: 74
Author(s): Wen Huang, Hasan Khatib
Software Mentions: 2
Published: almost 15 years ago
10.1186/s13073-015-0162-2
Transcriptomic landscape of lncRNAs in inflammatory bowel disease
Cited by: 134
Author(s): Aashiq H. Mirza, Claus Hb Berthelsen, Stefan E. Seemann, Xiaoyong Pan, Klaus Stensgaard Frederiksen, M. Vilien, Jan Gorodkin, Flemming Pociot
Software Mentions: 2
Published: over 9 years ago
10.1016/j.gpb.2019.03.001
Inulin Can Alleviate Metabolism Disorders in ob/ob Mice by Partially Restoring Leptin-related Pathways Mediated by Gut Microbiota
Cited by: 112
Author(s): Xiaofeng Song, Zhong Liu, Na Lyu, Fei Liu, Boxing Li, Yanan Hao, Yong Xue, Jing Li, Yuqing Feng, Yue Ma, Yongfei Hu, Baoli Zhu
Software Mentions: 2
Published: almost 6 years ago
10.1016/j.jaci.2017.08.044
Biallelic interferon regulatory factor 8 mutation: A complex immunodeficiency syndrome with dendritic cell deficiency, monocytopenia, and immune dysregulation
Cited by: 56
Author(s): Venetia Bigley, Sheetal Maisuria, Urszula Cytlak, Laura Jardine, Matthew A. Care, Kile Green, Merry Gunawan, Paul Milne, Rachel Dickinson, Sarah Wiscombe, David Parry, Rainer Döffinger, Arian Laurence, Claudia Fonseca, Oda Stoevesandt, Andrew R. Gennery, Andrew J. Cant, Reuben Tooze, A. John Simpson, Sophie Hambleton, Sinisa Savic, Gina M. Doody, Matthew Collin
Software Mentions: 2
Published: over 6 years ago
10.1186/1755-8794-6-S1-S12
Integrated lipidomics and transcriptomic analysis of peripheral blood reveals significantly enriched pathways in type 2 diabetes mellitus
Cited by: 46
Author(s): Chen Zhao, Jinghe Mao, Junmei Ai, Ming Shenwu, Tieliu Shi, Daqing Zhang, Xiaonan Wang, Yunliang Wang, Youping Deng
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.ppat.1002046
Transition of Plasmodium Sporozoites into Liver Stage-Like Forms Is Regulated by the RNA Binding Protein Pumilio
Cited by: 88
Author(s): Carina S. S. Gomes-Santos, Joanna A. M. Braks, Miguel Prudêncio, Céline Carret, Ana Gomes, Arnab Pain, Theresa Feltwell, Shahid M. Khan, Andrew P. Waters, Chris J. Janse, Gunnar R. Mair, Maria M. Mota
Software Mentions: 2
Published: over 13 years ago
10.1186/1471-2164-13-180
Genome wide response to dietary tetradecylthioacetic acid supplementation in the heart of Atlantic Salmon (Salmo salar L)
Cited by: 2
Author(s): Fabian Grammes, Kjell‐Arne Rørvik, Magny S. Thomassen, Rolf K. Berge, Harald Takle
Software Mentions: 2
Published: over 12 years ago
10.18632/oncotarget.12632
Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells
Cited by: 26
Author(s): Tong Zhou, Luke Erber, Bing Liu, Yankun Gao, Hai Bin Ruan, Yue Chen
Software Mentions: 2
Published: about 8 years ago
10.1186/s12864-016-2507-7
De novo assembly and analysis of the transcriptome of Ocimum americanum var. pilosum under cold stress
Cited by: 25
Author(s): Xiangqiang Zhan, Lan Yang, Jian Zhu, Zhaobo Lang
Software Mentions: 2
Published: over 8 years ago
10.1038/srep11938
Chromatin states modify network motifs contributing to cell-specific functions
Cited by: 10
Author(s): Hongying Zhao, Tingting Liu, Ling Liu, Guanxiong Zhang, Lin Pang, Fulong Yu, Huihui Fan, Yanyan Ping, Li Wang, Chaohan Xu, Yun Xiao, Xia Li
Software Mentions: 2
Published: over 9 years ago
10.1038/srep20127
Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals
Cited by: 87
Author(s): Alexandra Montagner, Agata Korecka, Arnaud Polizzi, Yannick Lippi, Yuna Blum, Cécile Canlet, Marie Tremblay-Franco, Amandine Gautier‐Stein, Rémy Burcelin, Yi-Chun Yen, H. Shawn Je, Maha Al-Asmakh, Gilles Mithieux, Velmurugesan Arulampalam, Sandrine Lagarrigue, Hervé Guillou, Sven Pettersson, Walter Wahli
Software Mentions: 2
Published: almost 9 years ago
10.1038/srep19729
Nucleosome architecture throughout the cell cycle
Cited by: 27
Author(s): Özgen Deniz, Oscar Flores, Martí Aldea, Montserrat Soler-López, Modesto Orozco
Software Mentions: 2
Published: almost 9 years ago
10.1038/srep27256
Induction of Germ Cell-like Cells from Porcine Induced Pluripotent Stem Cells
Cited by: 33
Author(s): Hanning Wang, Jinzhu Xiang, Wei Zhang, Junhong Li, Qingqing Wei, Zhong Liu, Hongsheng Ouyang, Jianyong Han
Software Mentions: 2
Published: over 8 years ago
10.1186/s12863-018-0606-y
Including gene networks to predict calving difficulty in Holstein, Brown Swiss and Jersey cattle
Cited by: 4
Author(s): Francesco Tiezzi, Maria E. Arceo, John B. Cole, Christian Maltecca
Software Mentions: 2
Published: over 6 years ago
10.1186/s12863-018-0673-0
Exome scale map of genetic alterations promoting metastasis in colorectal cancer
Cited by: 20
Author(s): Krzysztof Goryca, Maria Kulecka, Agnieszka Paziewska, Michalina Dąbrowska, Marta Grzelak, Magdalena Skrzypczak, Krzysztof Ginalski, Andrzej Mróz, Andrzej Rutkowski, Katarzyna Paczkowska, Michał Mikula, Jerzy Ostrowski
Software Mentions: 2
Published: about 6 years ago
10.1038/srep38864
Effect of dietary Astragalus Polysaccharide supplements on testicular miRNA expression profiles and enzymatic changes of breeder cocks
Cited by: 23
Author(s): Shengru Wu, Xiaochun Ren, Yulong Li, Wei Guo, Xinyu Lei, Junhu Yao, Xiaojun Yang
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12876-018-0752-8
Expression profiling and intracellular localization studies of the novel Proline-, Histidine-, and Glycine-rich protein 1 suggest an essential role in gastro-intestinal epithelium and a potential clinical application in colorectal cancer diagnostics
Cited by: 16
Author(s): Satu Oltedal, Ivar Skaland, Jodi Maple‐Grødem, Kjersti Tjensvoll, Emiel A. M. Janssen, Bjørnar Gilje, Rune Smaaland, Reino Heikkilä, Oddmund Nordgård
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-017-18370-2
ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks
Cited by: 53
Author(s): Sebastian Vlaic, Theresia Conrad, Christian Tokarski-Schnelle, Mika Gustafsson, Uta Dahmen, Reinhard Guthke, Stefan Schuster
Software Mentions: 2
Published: almost 7 years ago
10.1186/1471-2407-10-196
Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma
Cited by: 88
Author(s): Min‐Han Tan, Chin Fong Wong, Hwei Ling Tan, Ximing J. Yang, Jonathon A. Ditlev, Daisuke Matsuda, Sok Kean Khoo, Jun Sugimura, Tomoaki Fujioka, Kyle A. Furge, Eric J. Kort, Sophie Giraud, Sophie Ferlicot, Philippe Vielh, Delphine Amsellem-Ouazana, B Debré, T. Flam, Nicolas Thiounn, Marc Zerbib, Benoît Galand, S. Droupy, Vincent Molinié, Annick Vieillefond, Puay Hoon Tan, Stéphane Richard, Bin Tean Teh
Software Mentions: 2
Published: over 14 years ago
10.1038/s41598-018-36483-0
Analysis of Vibrio harveyi adaptation in sea water microcosms at elevated temperature provides insights into the putative mechanisms of its persistence and spread in the time of global warming
Cited by: 36
Author(s): Itxaso Montánchez, Elixabet Ogayar, Ander Hernández Plágaro, Anna Esteve‐Codina, Jèssica Gómez-Garrido, Maite Orruño, Inés Arana, Vladimir R. Kaberdin
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0084060
Whi3, an S. cerevisiae RNA-Binding Protein, Is a Component of Stress Granules That Regulates Levels of Its Target mRNAs
Cited by: 16
Author(s): Kristen J. Holmes, Daniel M. Klass, Evan L. Guiney, Martha S. Cyert
Software Mentions: 2
Published: almost 11 years ago
10.1038/s41598-019-46025-x
Dysfunctional MDR-1 disrupts mitochondrial homeostasis in the oocyte and ovary
Cited by: 11
Author(s): Haley Clark, Laura O. Knapik, Zijing Zhang, Xiaotian Wu, Mandar T. Naik, Nathalie Oulhen, Gary M. Wessel, Lynae M. Brayboy
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-48433-5
The regulation of the sulfur amino acid biosynthetic pathway in Cryptococcus neoformans: the relationship of Cys3, Calcineurin, and Gpp2 phosphatases
Cited by: 18
Author(s): Amanda Teixeira de Melo, Kevin Felipe Cruz Martho, Thiago Nunes Roberto, Erika Sayuri Nishiduka, Joel Machado, Otávio J. B. Brustolini, Alexandre Keiji Tashima, Ana Tereza Ribeiro de Vasconcelos, Marcelo A. Vallim, Renata C. Pascon
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-020-60235-8
Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction
Cited by: 8
Author(s): Jessica Gliozzo, Paolo Perlasca, Marco Mesiti, Elena Casiraghi, Viviana Vallacchi, Elisabetta Vergani, Giuliano Grossi, Alessandro Petrini, Matteo Ré, Alberto Paccanaro, Giorgio Valentini
Software Mentions: 2
Published: over 4 years ago
10.1186/s12915-021-01044-x
Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans
Cited by: 12
Author(s): Huifen Cao, Dongyang Xu, Ye Cai, Xueer Han, Lu Tang, Fan Gao, Yanfei Qi, Dingding Cai, Hong Wang, Maxim Ri, Денис Антонец, Yuri Vyatkin, Yue Chen, Xiang You, Fang Wang, Estelle Nicolas, Philipp Kapranov
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0011990
Gene Expression in Chicken Reveals Correlation with Structural Genomic Features and Conserved Patterns of Transcription in the Terrestrial Vertebrates
Cited by: 20
Author(s): Haisheng Nie, R.P.M.A. Crooijmans, A. Lammers, Evert M. van Schothorst, Jaap Keijer, Pieter Neerincx, Jack A. M. Leunissen, Hendrik‐Jan Megens, Martien A. M. Groenen
Software Mentions: 2
Published: over 14 years ago
10.1186/s12859-016-1387-9
Prior knowledge guided eQTL mapping for identifying candidate genes
Cited by: 0
Author(s): Yunli Wang, René Richard, Youlian Pan
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0071334
Expansion of Multipotent Stem Cells from the Adult Human Brain
Cited by: 38
Author(s): Wayne Murrell, Emily Palmero, John Bianco, Biljana Stangeland, Mrinal Joel, Linda Paulson, Bernd Thiede, Zanina Grieg, Ingunn Ramsnes, Håvard Kjesbu Skjellegrind, Ståle Nygård, Petter Brandal, Cecilie Sandberg, Einar O. Vik-Mo, Sheryl Palmero, Iver A. Langmoen
Software Mentions: 2
Published: over 11 years ago
10.1186/s13287-019-1303-0
Generation of pig induced pluripotent stem cells using an extended pluripotent stem cell culture system
Cited by: 43
Author(s): Junjun Xu, Lei Yu, Jianxiong Guo, Jinzhu Xiang, Zheng Zhang, Dengfeng Gao, Bingbo Shi, Haiyang Hao, Deling Jiao, Zhong Liu, Yu Wang, Jun Wu, Hong‐Jiang Wei
Software Mentions: 2
Published: over 5 years ago
10.1074/mcp.M115.048090
Characterization of the Tyrosine Kinase-Regulated Proteome in Breast Cancer by Combined use of RNA interference (RNAi) and Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) Quantitative Proteomics
Cited by: 15
Author(s): Justin Stebbing, Hua Zhang, Yang Xu, Arnhild Grothey, Paul Ajuh, Nicos Angelopoulos, Georgios Giamas
Software Mentions: 2
Published: about 9 years ago
10.15252/msb.20188266
Single‐cell <scp>mRNA</scp> profiling reveals the hierarchical response of mi <scp>RNA</scp> targets to mi <scp>RNA</scp> induction
Cited by: 20
Author(s): Andrzej J. Rzepiela, Souvik Ghosh, Jérémie Breda, Arnau Viña-Vilaseca, Afzal Pasha Syed, Andreas J. Gruber, Katja Eschbach, Christian Beisel, Erik van Nimwegen, Mihaela Zavolan
Software Mentions: 2
Published: over 6 years ago
10.1074/mcp.M116.065706
Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein–Protein Interactions
Cited by: 15
Author(s): Nikolaus Fortelny, Georgina S. Butler, Christopher M. Overall, Paul Pavlidis
Software Mentions: 2
Published: over 7 years ago
10.1186/s12920-021-01011-z
A method for cryopreservation and single nucleus RNA-sequencing of normal adult human interventricular septum heart tissue reveals cellular diversity and function
Cited by: 10
Author(s): Amy Larson, Michael T. Chin
Software Mentions: 2
Published: over 3 years ago
10.1186/s12859-018-2533-3
GOnet: a tool for interactive Gene Ontology analysis
Cited by: 169
Author(s): Mikhail Pomaznoy, Brendan Ha, Bjoern Peters
Software Mentions: 2
Published: almost 6 years ago
10.1186/s11658-018-0110-4
Systematic identification of the key candidate genes in breast cancer stroma
Cited by: 29
Author(s): Yanxia Wang, Hui Xu, Baoan Zhu, Qiu Zhen-ling, Lin Zx
Software Mentions: 2
Published: about 6 years ago
10.1186/1471-2105-11-S9-S11
Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models
Cited by: 4
Author(s): Xinan Yang, Younghee Lee, Yong Huang, James L. Chen, Rosie Hongmei Xing, Yves A. Lussier
Software Mentions: 2
Published: about 14 years ago
10.1186/s13229-017-0151-y
A brain proteomic investigation of rapamycin effects in the Tsc1 +/− mouse model
Cited by: 18
Author(s): Hendrik Wesseling, Ype Elgersma, Sabine Bahn
Software Mentions: 2
Published: over 7 years ago
10.3390/cells9092098
Identification and Comparison of Hyperglycemia-Induced Extracellular Vesicle Transcriptome in Different Mouse Stem Cells
Cited by: 7
Author(s): Grace Huang, Venkata Naga Srikanth Garikipati, Yan Zhou, Cynthia Benedict, Steven R. Houser, Walter J. Koch, Raj Kishore
Software Mentions: 2
Published: about 4 years ago
10.3390/cells10092477
Detection of Novel Potential Regulators of Stem Cell Differentiation and Cardiogenesis through Combined Genome-Wide Profiling of Protein-Coding Transcripts and microRNAs
Cited by: 1
Author(s): Rui S. R. Machado, Agapios Sachinidis, Matthias E. Futschik
Software Mentions: 2
Published: about 3 years ago
10.1186/s13148-016-0273-7
Global DNA methylation patterns in Barrett’s esophagus, dysplastic Barrett’s, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use
Cited by: 25
Author(s): Andrew M. Kaz, Chao Jen Wong, Vinay Varadan, Joseph E. Willis, Amitabh Chak, William M. Grady
Software Mentions: 2
Published: about 8 years ago
10.1186/1471-2164-9-346
Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region
Cited by: 50
Author(s): Martin Kircher, Christoph Bock, Martina Paulsen
Software Mentions: 2
Published: over 16 years ago
10.1128/mSystems.00165-18
Persistent Interactions with Bacterial Symbionts Direct Mature-Host Cell Morphology and Gene Expression in the Squid-Vibrio Symbiosis
Cited by: 13
Author(s): Natacha Kremer, Eric J. Koch, Adil El Filali, Lawrence Zhou, Elizabeth A. C. Heath‐Heckman, Edward G. Ruby, Margaret J. McFall‐Ngai
Software Mentions: 2
Published: about 6 years ago
10.1186/1471-2105-10-262
Integrative modeling of transcriptional regulation in response to antirheumatic therapy
Cited by: 36
Author(s): Michael Hecker, Robert Goertsches, Robby Engelmann, Hans‐Juergen Thiesen, Reinhard Guthke
Software Mentions: 2
Published: about 15 years ago
10.1186/1471-2105-9-305
MAID : An effect size based model for microarray data integration across laboratories and platforms
Cited by: 13
Author(s): Ivan Borozan, Limin Chen, Bryan Paeper, Jenny Heathcote, A.M. Edwards, Michael A. Katze, Zhaolei Zhang, Ian McGilvray
Software Mentions: 2
Published: over 16 years ago
10.1371/journal.pgen.1006595
Genome-wide exonic small interference RNA-mediated gene silencing regulates sexual reproduction in the homothallic fungus Fusarium graminearum
Cited by: 51
Author(s): Hokyoung Son, Ae Ran Park, Jae Yun Lim, Chanseok Shin, Yin-Won Lee
Software Mentions: 2
Published: almost 8 years ago
10.1186/1471-2105-14-353
The causal effect of red blood cell folate on genome-wide methylation in cord blood: a Mendelian randomization approach
Cited by: 22
Author(s): Alexandra M. Binder, Karin B. Michels
Software Mentions: 2
Published: almost 11 years ago
10.1155/2014/396727
Gender-Specific DNA Methylome Analysis of a Han Chinese Longevity Population
Cited by: 9
Author(s): Liang Sun, Jie Lin, Hongwu Du, Chengping Hu, Zezhi Huang, Zhen Lv, Chenguang Zheng, Xiaoyi Shi, Yan Zhang, Ze Yang
Software Mentions: 2
Published: almost 11 years ago
10.3390/ijms19010234
Transcriptomics Evidence for Common Pathways in Human Major Depressive Disorder and Glioblastoma
Cited by: 13
Author(s): Yongfang Xie, Ling Wang, Zengyan Xie, Chuisheng Zeng, Kunxian Shu
Software Mentions: 2
Published: almost 7 years ago
10.1002/ece3.5728
Gene expression response to a nematode parasite in novel and native eel hosts
Cited by: 14
Author(s): Seraina E. Bracamonte, Paul R. Johnston, Michael T. Monaghan, Klaus Knopf
Software Mentions: 2
Published: about 5 years ago
10.1002/ece3.447
Early gene expression divergence between allopatric populations of the house mouse ( <i>Mus musculus domesticus</i> )
Cited by: 17
Author(s): Jarosław Bryk, Mehmet Somel, Anna Lorenc, Meike Teschke
Software Mentions: 2
Published: almost 12 years ago
10.1186/1471-2164-10-461
Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae
Cited by: 53
Author(s): Eija Rintala, Mervi Toivari, Juha-Pekka Pitkänen, Marilyn G. Wiebe, Laura Ruohonen, Merja Penttilä
Software Mentions: 2
Published: almost 16 years ago
10.1186/1471-2164-14-609
Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species
Cited by: 20
Author(s): Hua Bao, Arun Kommadath, Xinwei Sun, Yan Meng, Adriano S. Arantes, Graham Plastow, Le Luo Guan, Paul Stothard
Software Mentions: 2
Published: about 11 years ago
10.1186/s40001-019-0381-x
Identification of key genes involved in myocardial infarction
Cited by: 21
Author(s): Linlin Qiu, Xueqing Liu
Software Mentions: 2
Published: over 5 years ago
10.1038/s12276-019-0267-6
IRF1 is critical for the TNF-driven interferon response in rheumatoid fibroblast-like synoviocytes
Cited by: 39
Author(s): Michael Bonelli, K Dalwigk, Alexander Platzer, Isabel Olmos Calvo, Silvia Hayer, Birgit Niederreiter, Johannes Holinka, Florian Sevelda, Thomas Pap, Günter Steiner, Giulio Superti‐Furga, Josef S Smolen, Hans P. Kiener, Thomas Karonitsch
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0014199
Multiple Roles for the Non-Coding RNA SRA in Regulation of Adipogenesis and Insulin Sensitivity
Cited by: 161
Author(s): Bin Xu, Isabelle Gerin, Hongzhi Miao, Dang Vu-Phan, Craig Johnson, Ruichuan Xu, Xiao Wei Chen, William P. Cawthorn, Ormond A. MacDougald, Ronald J. Koenig
Software Mentions: 2
Published: almost 14 years ago
10.1371/journal.pone.0125934
Evaluation of iTRAQ and SWATH-MS for the Quantification of Proteins Associated with Insulin Resistance in Human Duodenal Biopsy Samples
Cited by: 41
Author(s): Sylvie Bourassa, Frédéric Fournier, Benjamin Nehmé, Isabelle Kelly, André Tremblay, Valéry Lemelin, Benoı̂t Lamarche, Patrick Couture, Arnaud Droit
Software Mentions: 2
Published: over 9 years ago
10.3389/fgene.2013.00309
Multi-omic network signatures of disease
Cited by: 19
Author(s): David L. Gibbs, Lisa E. Gralinski, Ralph S. Baric, Shannon K. McWeeney
Software Mentions: 2
Published: almost 11 years ago
10.3389/fgene.2021.637755
Comprehensive Analysis of Aerobic Exercise-Related Genes Identifies CDCA4 That Promotes the Progression of Osteosarcoma
Cited by: 4
Author(s): Suyu Hao, Jun Zhu, Xinyue Zhang, Jingyue Qiu, Xuan Qin, Liping Ye
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12860-020-00268-z
PGRMC1 effects on metabolism, genomic mutation and CpG methylation imply crucial roles in animal biology and disease
Cited by: 14
Author(s): Bashar M. Thejer, Partho P. Adhikary, Sarah L. Teakel, Johnny Fang, Paul A. Weston, Saliya Gurusinghe, Ayad G. Anwer, Martin E. Gosnell, Jalal Jazayeri, Marina Ludescher, Lesley-Ann Gray, Michael Pawlak, Robyn H. Wallace, Sameer D. Pant, Marie Wong, Tamás Fischer, Elizabeth J. New, Tanja Fehm, Hans Neubauer, Ewa M. Goldys, Jane C. Quinn, Leslie A. Weston, Michael A. Cahill
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0055522
Low SP1 Expression Differentially Affects Intestinal-Type Compared with Diffuse-Type Gastric Adenocarcinoma
Cited by: 18
Author(s): Hun Seok Lee, Cheol-Keun Park, Ensel Oh, Özgür Cem Erkín, Hun Soon Jung, Mi-Hyun Cho, Mi Kwon, Seoung Wan Chae, Seok-Hyung Kim, Lihui Wei, Min-Jeong Park, Su-Yeon Lee, Hyun-Kwon Yang, Lei Jia, Yoon–La Choi, Young Kee Shin
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0173300
Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut
Cited by: 12
Author(s): Alix Armero, Luc Baudouin, Stéphanie Bocs, Dominique This
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0124562
Pluripotent and Metabolic Features of Two Types of Porcine iPSCs Derived from Defined Mouse and Human ES Cell Culture Conditions
Cited by: 30
Author(s): Wei Zhang, Yangli Pei, Zhong Liu, Bingqiang Wen, Suying Cao, Jianyong Han
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0021503
siRNA Off-Target Effects Can Be Reduced at Concentrations That Match Their Individual Potency
Cited by: 75
Author(s): Daniel R. Caffrey, Juan Zhao, Zhili Song, Michael Schäffer, Steven Haney, Romesh R. Subramanian, Albert B. Seymour, Jason D. Hughes
Software Mentions: 2
Published: over 13 years ago
10.3389/fnmol.2017.00445
Regulation of Adult CNS Axonal Regeneration by the Post-transcriptional Regulator Cpeb1
Cited by: 6
Author(s): Wilson Pak-Kin Lou, Álvaro Mateos, Marta Koch, Stefan Klussman, Chao Yang, Na Lü, Sachin Kumar, Stefanie Limpert, Manuel Göpferich, Marlen Zschaetzsch, Christopher Sliwinski, Marc Kenzelmann, Matthias Seedorf, Carlos Maillo, Elena Senís, Dirk Grimm, Radhika Puttagunta, Raúl Méndez, Kai Liu, Bassem A. Hassan, Ana Martin‐Villalba
Software Mentions: 2
Published: almost 7 years ago
10.3389/fphys.2017.00723
N-acetylcysteine Counteracts Adipose Tissue Macrophage Infiltration and Insulin Resistance Elicited by Advanced Glycated Albumin in Healthy Rats
Cited by: 10
Author(s): Karolline S. da Silva, Paula Ramos Pinto, N. Fabre, Diogo Bugano Diniz Gomes, Karina Thieme, Lígia Shimabukuro Okuda, Rodrigo Tallada Iborra, Vanessa G. Freitas, Maria Heloísa Massola Shimizu, Walcy Rosolia Teodoro, Suely Kazue Nagahashi Marie, Tom M. Woods, Margaret A. Brimble, Russell Pickford, Kerry‐Anne Rye, Maristela Mitiko Okamoto, Sérgio Catanozi, Maria L. Correa-Giannela, Ubiratan Fabres Machado, Marisa Passarelli
Software Mentions: 2
Published: about 7 years ago
10.18632/oncotarget.8504
ATG9A loss confers resistance to trastuzumab via c-Cbl mediated Her2 degradation
Cited by: 20
Author(s): João Nunes, Hua Zhang, Nicos Angelopoulos, Jyoti Chhetri, Clodia Osipo, Arnhild Grothey, Justin Stebbing, Georgios Giamas
Software Mentions: 2
Published: over 8 years ago
10.1534/g3.114.013904
Genomic Analysis of the Pacific Oyster (<i>Crassostrea gigas</i>) Reveals Possible Conservation of Vertebrate Sex Determination in a Mollusc
Cited by: 66
Author(s): Na Zhang, Fei Xu, Ximing Guo
Software Mentions: 2
Published: about 10 years ago
10.1186/1471-2164-14-656
FGF2-induced effects on transcriptome associated with regeneration competence in adult human fibroblasts
Cited by: 36
Author(s): Olga Kashpur, David S. Lapointe, Sakthikumar Ambady, Elizabeth F. Ryder, Tanja Dominko
Software Mentions: 2
Published: about 11 years ago
10.1534/g3.119.400947
Forebrain Transcriptional Response to Transient Changes in Circulating Androgens in a Cichlid Fish
Cited by: 2
Author(s): Ana S. Félix, Sara D. Cardoso, António Roleira, Rui Filipe Oliveira
Software Mentions: 2
Published: over 4 years ago
10.1186/gb-2007-8-4-r63
Global analyses of mRNA translational control during early Drosophila embryogenesis
Cited by: 79
Author(s): Xiaoli Qin, Soyeon Ahn, Terence P. Speed, Gerald M. Rubin
Software Mentions: 2
Published: almost 18 years ago
10.1371/journal.pone.0081702
Mycophenolic Acid Inhibits Migration and Invasion of Gastric Cancer Cells via Multiple Molecular Pathways
Cited by: 36
Author(s): Boying Dun, Ashok Sharma, Yong Teng, Haitao Liu, Sharad Purohit, Heng Xu, Lingwen Zeng, Jin Xiong She
Software Mentions: 2
Published: about 11 years ago
10.1186/s40478-016-0334-3
Analysis of primary visual cortex in dementia with Lewy bodies indicates GABAergic involvement associated with recurrent complex visual hallucinations
Cited by: 55
Author(s): Ahmad Khundakar, Peter S. Hanson, Daniel Erskine, Nichola Z. Lax, Joseph Roscamp, Evangelia Karyka, Eliona Tsefou, Preeti Singh, Simon Cockell, Andrew Gribben, Lynne Ramsay, Peter G. Blain, Urs Peter Mosimann, Deborah Lett, Matthias Elstner, Doug M. Turnbull, Charles Xiang, Michael J. Brownstein, John T. O’Brien, John‐Paul Taylor, Johannes Attems, Alan Thomas, Ian G. McKeith, Christopher M. Morris
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0017940
Acute Endotoxin-Induced Thymic Atrophy Is Characterized By Intrathymic Inflammatory and Wound Healing Responses
Cited by: 61
Author(s): Matthew J. Billard, Amanda Louise Gruver, Gregory D. Sempowski
Software Mentions: 2
Published: over 13 years ago
10.1186/1471-2164-11-151
Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements
Cited by: 29
Author(s): Danilo Licastro, Vincenzo A. Gennarino, Francesca Petrera, Remo Sanges, Sandro Banfi, Elia Stupka
Software Mentions: 2
Published: over 14 years ago