bioconductor: ArrayExpress | Projects

10.1186/2047-783X-18-44

RETRACTED ARTICLE: Gene expression profiling analysis of hepatocellular carcinoma
Cited by: 4
Author(s): Deyong Kong, Heming Chen, Weiqun Chen, Shuiyi Liu, Hui Wang, Tangwei Wu, Hongda Lu, Qing Kong, Xiaodong Huang, Zhongxin Lu
Software Mentions: 3
Published: over 12 years ago

10.1111/j.1525-142X.2010.00400.x

Molecular signaling in zebrafish development and the vertebrate phylotypic period
Cited by: 37
Author(s): Aurélie Comte, Julien Roux, Marc Robinson‐Rechavi
Software Mentions: 3
Published: over 16 years ago

10.3390/microarrays5030023

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories
Cited by: 9
Author(s): Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
Software Mentions: 3
Published: over 9 years ago

10.15252/emmm.201606711

Gene signature driving invasive mucinous adenocarcinoma of the lung
Cited by: 72
Author(s): Minzhe Guo, Koichi Tomoshige, Michael Meister, Thomas Muley, Takuya Fukazawa, Tomoshi Tsuchiya, Rebekah Karns, Arne Warth, Iris M. Fink-Baldauf, Takeshi Nagayasu, Yoshio Naomoto, Yan Xu, Marcus Mall, Yutaka Maeda
Software Mentions: 3
Published: over 9 years ago

10.3390/metabo11040221

Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling
Cited by: 5
Author(s): Özlem Altay, Cheng Cheng Zhang, Hasan Türkez, Jens Nielsen, Mathias Uhlén, Adil Mardinoğlu
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pntd.0005559

MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni
Cited by: 32
Author(s): Anna V. Protasio, Stijn van Dongen, Julie Collins, Leonor Quintais, Diogo M Ribeiro, Florian Sessler, Martin Hunt, Gabriel Rinaldi, James J. Collins, Anton J. Enright, Matthew Berriman
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pntd.0008059

Exposure of Anopheles mosquitoes to trypanosomes reduces reproductive fitness and enhances susceptibility to Plasmodium
Cited by: 10
Author(s): Constentin Dieme, Natalia Marta Zmarlak, Emma Brito-Fravallo, Christelle Travaillé, Adrien Pain, Floriane Cherrier, Corinne Genève, Estefanía Calvo-Álvarez, Michelle M. Riehle, Kenneth D. Vernick, Brice Rotureau, Christian Mitri
Software Mentions: 3
Published: over 6 years ago

10.1093/database/bay003

TISSUES 2.0: an integrative web resource on mammalian tissue expression
Cited by: 110
Author(s): Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen
Software Mentions: 3
Published: over 8 years ago

10.18632/aging.103073

MicroRNA-375 exacerbates knee osteoarthritis through repressing chondrocyte autophagy by targeting ATG2B
Cited by: 30
Author(s): Hongxing Li, Zhiling Li, Yigang Pi, Yang Chen, Lin Mei, Yiliao Luo, Jingping Xie, Xinzhan Mao
Software Mentions: 3
Published: about 6 years ago

10.1093/database/baab006

Curation of over 10 000 transcriptomic studies to enable data reuse
Cited by: 18
Author(s): Nathaniel Lim, Stepan Tesar, Manuel Belmadani, Guillaume Poirier-Morency, B. Ogan Mancarci, Jordan Sicherman, Matthew P. Jacobson, Justin Leong, Pei‐Hua Tan, Paul Pavlidis
Software Mentions: 3
Published: over 5 years ago

10.1016/j.devcel.2019.05.020

Drosophila Ovarian Germline Stem Cell Cytocensor Projections Dynamically Receive and Attenuate BMP Signaling
Cited by: 25
Author(s): Scott G. Wilcockson, Hilary L. Ashe
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-018-5176-x

funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data
Cited by: 5
Author(s): Liis Kolberg, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-494

Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast
Cited by: 2
Author(s): Lucas D. Ward, Junbai Wang, Harmen J. Bussemaker
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pgen.1003067

CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function
Cited by: 102
Author(s): Jacy L. Wagnon, Michael Briese, Wenzhi Sun, Connie L. Mahaffey, Tomaž Curk, Gregor Rot, Jernej Ule, Wayne N. Frankel
Software Mentions: 3
Published: over 13 years ago

10.1007/s00262-020-02718-1

Immune checkpoint-related serum proteins and genetic variants predict outcomes of localized prostate cancer, a cohort study
Cited by: 35
Author(s): Qinchuan Wang, Yuanqing Ye, Hao Yu, Shu-Hong Lin, Huakang Tu, Dong Liang, David W. Chang, Maosheng Huang, Xifeng Wu
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2105-13-S14-S5

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis
Cited by: 12
Author(s): Ivan Merelli, Federica Viti, Luciano Milanesi
Software Mentions: 3
Published: almost 14 years ago

10.1093/database/bay011

BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology
Cited by: 23
Author(s): Kleanthi Lakiotaki, Nikolaos Vorniotakis, Michail Tsagris, Γεώργιος Γεωργακόπουλος, Ioannis Tsamardinos
Software Mentions: 3
Published: over 8 years ago

10.1093/database/baz106

Enabling semantic queries across federated bioinformatics databases
Cited by: 22
Author(s): Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson‐Rechavi, Christophe Dessimoz
Software Mentions: 3
Published: over 7 years ago

10.1186/s12935-021-01932-w

SNRPD1 confers diagnostic and therapeutic values on breast cancers through cell cycle regulation
Cited by: 7
Author(s): Xiaofeng Dai, Lihui Yu, Xiao Chen, Jianying Zhang
Software Mentions: 3
Published: about 5 years ago

10.1155/2012/650842

ArraySearch: A Web-Based Genomic Search Engine
Cited by: 1
Author(s): Tyler J. Wilson, Xijin Ge
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pgen.0040014

Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules
Cited by: 481
Author(s): Todd P. Michael, Todd C. Mockler, Ghislaı̀n Breton, Connor McEntee, Amanda Byer, Jonathan D. Trout, Samuel P. Hazen, Rongkun Shen, Henry D. Priest, Christopher Sullivan, Scott A. Givan, Marcelo J. Yanovsky, Fangxin Hong, Steve A. Kay, Joanne Chory
Software Mentions: 3
Published: over 18 years ago

10.1186/s12859-020-3364-6

Detection of suspicious interactions of spiking covariates in methylation data
Cited by: 0
Author(s): Miriam Sieg, Gregor Richter, Arne S. Schäefer, Jochen Kruppa
Software Mentions: 3
Published: over 6 years ago

10.1016/j.dib.2020.106604

RNA-Seq transcriptome data of human cells infected with influenza A/Puerto Rico/8/1934 (H1N1) virus
Cited by: 6
Author(s): Evgenii Zhuravlev, Mariia Sergeeva, Sergey Malanin, Р. Н. Амирханов, Dmitriy V. Semenov, Tatiana V. Grigoryeva, Andrey Komissarov, Г. А. Степанов
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-11-27

Genomics Portals: integrative web-platform for mining genomics data
Cited by: 13
Author(s): Kaustubh Shinde, Mukta Phatak, Johannes M. Freudenberg, Jing Chen, Qian Li, Joshi K Vineet, Zhen Hu, Krishnendu Ghosh, Jarosław Meller, Mario Medvedovic
Software Mentions: 3
Published: over 16 years ago

10.1093/bib/bby051

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application
Cited by: 103
Author(s): Gaye Lightbody, Valeriia Haberland, Fiona Browne, Laura E. Taggart, Huiru Zheng, Eileen E. Parkes, Jaine K. Blayney
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0142443

Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma
Cited by: 9
Author(s): Abhinav Kaushik, Yashuma Bhatia, Shakir Ali, Dinesh Gupta
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-019-5748-4

Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets
Cited by: 1
Author(s): Dirkjan Schokker, Ina Hulsegge, H. Woelders, Johanna M.J. Rebel
Software Mentions: 3
Published: about 7 years ago

10.1186/bcr3020

Genomic and phenotypic analysis of BRCA2mutated breast cancers reveals co-occurring changes linked to progression
Cited by: 22
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Katrín Ólafsdóttir, Hörður Bjarnason, Óskar T. Jóhannsson, Sigrídur K. Bödvarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 3
Published: over 14 years ago

10.1186/bcr2926

Identification of germline alterations of the mad homology 2 domain of SMAD3 and SMAD4 from the Ontario site of the breast cancer family registry (CFR)
Cited by: 17
Author(s): Eric Tram, Irada Ibrahim‐Zada, Laurent Briollais, Julia A. Knight, Irene L. Andrulis, Hilmi Özçelik
Software Mentions: 3
Published: almost 15 years ago

10.1186/s12859-019-2912-4

TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Cited by: 2
Author(s): Salvatore Alaimo, Annalisa Di Maria, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1005250

Genetic Regulation of Bone Metabolism in the Chicken: Similarities and Differences to Mammalian Systems
Cited by: 41
Author(s): Martin Johnsson, Kenneth B. Jonsson, Leif C. Andersson, Per Jensen, I. A. Wright
Software Mentions: 3
Published: about 11 years ago

10.1002/cam4.1633

Molecular heterogeneity in human papillomavirus‐dependent and ‐independent vulvar carcinogenesis
Cited by: 16
Author(s): Dorian R.A. Swarts, Quirinus J.M. Voorham, Annina P. van Splunter, Saskia M. Wilting, Daoud Sie, Divera T.M. Pronk, Marc van Beurden, Daniëlle A.M. Heideman, Peter J.F. Snijders, Chris J.L.M. Meijer, Renske D.M. Steenbergen, Maaike Bleeker
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0228314

Influence of heat stress on reference genes stability in heart and liver of two chickens genotypes
Cited by: 5
Author(s): Juliana Gracielle Gonzaga Gromboni, Hellenn Cardoso Oliveira, Daniele Botelho Diniz Marques, Adriana García, Ronaldo Vasconcelos Farias Filho, Caio Fernando Gromboni, Teillor Machado Souza, Amauri Arias Wenceslau
Software Mentions: 3
Published: over 6 years ago

10.1007/s12263-014-0439-x

White adipose tissue reference network: a knowledge resource for exploring health-relevant relations
Cited by: 10
Author(s): Thomas Kelder, Georg Summer, Martien P. M. Caspers, Evert M. van Schothorst, Jaap Keijer, Loes P. M. Duivenvoorde, К. Schimrigk, Anja Voigt, Laura Bohnert, Catalina Picó, M. Luisa Bonet, A. Dembińska-Kieć, Małgorzata Malczewska-Malec, Beata Kieć‐Wilk, Josep Maria del Bas, Antoni Caimari, Lluı́s Arola, Marjan van Erk, Ben van Ommen, Marijana Radonjić
Software Mentions: 3
Published: over 11 years ago

10.1155/2020/5943014

Bioinformatic Identification of Neuroblastoma Microenvironment-Associated Biomarkers with Prognostic Value
Cited by: 4
Author(s): Yi Wang, Huan Luo, Jing Cao, Chi Ma
Software Mentions: 3
Published: almost 6 years ago

10.3389/fphar.2019.00198

A Meta-Analysis of the Performance of a Blood-Based Exposure Response Gene Signature Across Clinical Studies on the Tobacco Heating System 2.2 (THS 2.2)
Cited by: 2
Author(s): Florian Martin, Marja Talikka, Nikolai V. Ivanov, Christelle Haziza, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-12989-x

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells
Cited by: 62
Author(s): Simone Rizzetto, Auda A. Eltahla, Peijie Lin, Rowena A. Bull, Andrew R. Lloyd, Joshua W. K. Ho, Vanessa Venturi, Fabio Luciani
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-017-17730-2

Constitutively elevated levels of SOCS1 suppress innate responses in DF-1 immortalised chicken fibroblast cells
Cited by: 28
Author(s): Efstathios S. Giotis, CS Ross, RC Robey, Axel Nohturfft, Stephen Goodbourn, Michael A. Skinner
Software Mentions: 3
Published: over 8 years ago

10.1155/2014/345106

Comparison of Merging and Meta-Analysis as Alternative Approaches for Integrative Gene Expression Analysis
Cited by: 45
Author(s): Jonatan Taminau, Cosmin Lazar, Stijn Meganck, Ann Nowé
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-019-49410-8

Spodoptera frugiperda transcriptional response to infestation by Steinernema carpocapsae
Cited by: 13
Author(s): Louise Huot, Simon C. George, Pierre-Alain Girard, Dany Séverac, Nicolas Nègre, Bernard Duvic
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-22284-y

Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis
Cited by: 19
Author(s): Li Jin, Peng Yu
Software Mentions: 3
Published: over 8 years ago

10.7150/jca.60647

FOXD3-induced miR-133a blocks progression and metastasis of colorectal cancer through regulating UBA2
Cited by: 4
Author(s): Yuanfang Cheng, Yajuan Wang, Yuanzun Cheng, Qingmei Yang, Lejing Zhang, Zhaoxi Li, Jiancheng Cheng
Software Mentions: 3
Published: over 5 years ago

10.3389/fphys.2019.00433

Increasing Upstream Chromatin Long–Range Interactions May Favor Induction of Circular RNAs in LysoPC-Activated Human Aortic Endothelial Cells
Cited by: 16
Author(s): Angus Li, Yu Sun, Charles Drummer, Yifan Lu, Daohai Yu, Yan Zhou, Xinyuan Li, Simone J. Pearson, Candice Johnson, Catherine C. Yu, William Y. Yang, Kevin Mastascusa, Xiaohua Jiang, Jianxin Sun, Thomas J. Rogers, Wenhui Hu, Hong Wang, Xiaofeng Yang
Software Mentions: 3
Published: about 7 years ago

10.1038/s41597-019-0046-1

Navigating in vitro bioactivity data by investigating available resources using model compounds
Cited by: 1
Author(s): Sten Ilmjärv, Fiona Augsburger, Jerven Bolleman, Robin Liechti, Alan Bridge, Jenny Sandström, Vincent Jaquet, Ioannis Xenarios, Karl-Heinz Krause
Software Mentions: 3
Published: about 7 years ago

10.3389/fphys.2018.00618

Coactivation of TLR2 and TLR8 in Primary Human Monocytes Triggers a Distinct Inflammatory Signaling Response
Cited by: 14
Author(s): Korbinian Bösl, Miriam S. Giambelluca, Markus Haug, Marit Bugge, Terje Espevik, Richard K. Kandasamy, Bjarte Bergstrøm
Software Mentions: 3
Published: about 8 years ago

10.1038/s41597-019-0011-z

Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley
Cited by: 21
Author(s): Camilla Beate Hill, Debbie Wong, Josquin Tibbits, Kerrie Forrest, Matthew Hayden, Xiaoqi Zhang, Sharon Westcott, Tefera Tolera Angessa, Chengdao Li
Software Mentions: 3
Published: about 7 years ago

10.3389/fimmu.2019.02136

Identification and Characterization of Post-activated B Cells in Systemic Autoimmune Diseases
Cited by: 37
Author(s): Sarah Y. Weißenberg, Franziska Szelinski, Eva Schrezenmeier, Ana‐Luisa Stefanski, Annika Wiedemann, Héctor Rincón‐Arévalo, Anna Welle, Annemarie Jungmann, Karl Nordström, Jörn Walter, Juliana Imgenberg‐Kreuz, Gunnel Nordmark, Lars Rönnblom, Prathyusha Bachali, Michelle D. Catalina, Amrie C. Grammer, Peter E. Lipsky, Andreia C. Lino, Thomas Dörner
Software Mentions: 3
Published: over 6 years ago

10.1128/mSystems.00025-15

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions
Cited by: 111
Author(s): Jie Tan, John H. Hammond, Deborah A. Hogan, Casey S. Greene
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-018-25085-5

RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells
Cited by: 67
Author(s): Anda R. Gliga, Sebastiano Di Bucchianico, Jessica M. Lindvall, Bengt Fadeel, Hanna Karlsson
Software Mentions: 3
Published: about 8 years ago

10.1128/mSphere.00305-16

Coordinate Regulation of Antimycin and Candicidin Biosynthesis
Cited by: 34
Author(s): Thomas C McLean, Paul A. Hoskisson, Ryan F. Seipke
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.53944

Loss of centromere function drives karyotype evolution in closely related Malassezia species
Cited by: 37
Author(s): Sundar Ram Sankaranarayanan, Giuseppe Ianiri, Marco A. Coelho, Hashim Reza, Bhagya C. Thimmappa, Promit Ganguly, Rakesh Netha Vadnala, Sheng Sun, Rahul Siddharthan, Christian Tellgren-Roth, Thomas L. Dawson, Joseph Heitman, Kaustuv Sanyal
Software Mentions: 3
Published: over 6 years ago

10.1038/sdata.2018.198

RNA-seq of macrophages of amoeboid or mesenchymal migratory phenotype due to specific structure of environment
Cited by: 13
Author(s): Vladimı́r Čermák, Aneta Gandalovičová, Ladislav Merta, Jitka Fučíková, Radek Špíšek, Daniel Rösel, Jan Brábek
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-26170-5

Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions
Cited by: 6
Author(s): David Talavera, Christopher J. Kershaw, Joseph L. Costello, Lydia M. Castelli, William Rowe, Paul F. G. Sims, Mark P. Ashe, Chris M. Grant, Graham D. Pavitt, Simon J. Hubbard
Software Mentions: 3
Published: about 8 years ago

10.1128/mBio.02684-19

Contextual Flexibility in Pseudomonas aeruginosa Central Carbon Metabolism during Growth in Single Carbon Sources
Cited by: 49
Author(s): Stephen K. Dolan, Michael Kohlstedt, Stephen Trigg, Pedro P. Vallejo Ramirez, Clemens F. Kaminski, Christoph Wittmann, Martin Welch
Software Mentions: 3
Published: about 6 years ago

10.1128/mBio.01871-18

Structural and Nonstructural Genes Contribute to the Genetic Diversity of RNA Viruses
Cited by: 27
Author(s): Natalie D. Collins, Andrew S. Beck, Steven G. Widen, Thomas G. Wood, Stephen Higgs, Alan D.T. Barrett
Software Mentions: 3
Published: over 7 years ago

10.1186/s13395-015-0059-1

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging
Cited by: 72
Author(s): Jing Su, Carl Johan Ekman, Nikolay Oskolkov, Leo Lahti, Kristoffer Ström, Alvis Brāzma, Leif Groop, Johan Rung, Ola Hansson
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-018-35868-5

In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors
Cited by: 11
Author(s): Suzanne Vanhauwaert, Bieke Decaesteker, Sara De Brouwer, Carina Leonelli, Kaat Durinck, Pieter Mestdagh, Jo Vandesompele, Karen Sermon, Geertrui Denecker, Christophe Van Neste, Franki Speleman, Katleen De Preter
Software Mentions: 3
Published: over 7 years ago

10.3389/fcell.2021.642697

Tlx3 Exerts Direct Control in Specifying Excitatory Over Inhibitory Neurons in the Dorsal Spinal Cord
Cited by: 3
Author(s): Filipe Almeida Monteiro, Rafael Mendes Miranda, Marta C Samina, Ana Cristina Dias, Alexandre A.S.F. Raposo, Patrícia Oliveira, Carlos Reguenga, Diogo S. Castro, Deolinda Lima
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-27258-8

A data mining paradigm for identifying key factors in biological processes using gene expression data
Cited by: 13
Author(s): Jin Li, Le Zheng, Akihiko Uchiyama, Lianghua Bin, Theodora M. Mauro, Peter M. Elias, Tadeusz Pawełczyk, Monika Sakowicz-Burkiewicz, Magdalena Trzeciak, Donald Y.M. Leung, María I. Morasso, Peng Yu
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.31362

A tissue-specific, Gata6-driven transcriptional program instructs remodeling of the mature arterial tree
Cited by: 11
Author(s): Marta Losa, Víctor Latorre, Munazah Andrabi, Franck Ladam, Charles G. Sagerström, Ana Nóvoa, Peyman Zarrineh, Laure Bridoux, Neil A. Hanley, Bernard Malissen, Nicoletta Bobola
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.38309

High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect
Cited by: 41
Author(s): Daniel Medina-Cano, Ekin Ucuncu, Lam Son Nguyen, Michaël Nicouleau, Joanna Lipecka, Jean-Charles Bizot, Christian Thiel, François Foulquier, Nathalie Lefort, Catherine Faivre‐Sarrailh, Laurence Colleaux, Ida Chiara Guerrera, Vincent Cantagrel
Software Mentions: 3
Published: over 7 years ago

10.1186/2043-9113-2-22

mCOPA: analysis of heterogeneous features in cancer expression data
Cited by: 18
Author(s): Chenwei Wang, Alperen Taciroglu, Stefan Maetschke, Colleen C. Nelson, Mark A. Ragan, Melissa J. Davis
Software Mentions: 3
Published: over 14 years ago

10.3389/fncel.2020.599152

Intrinsically Self-renewing Neuroprogenitors From the A/J Mouse Spiral Ganglion as Virtually Unlimited Source of Mature Auditory Neurons
Cited by: 7
Author(s): Francis Rousset, Vivianne Beatrix Christina Kokje, Rebecca Sipione, Dominik Schmidbauer, German Nacher-Soler, Sten Ilmjärv, Marta Coelho, Stefan Fink, François Voruz, Antoun El Chemaly, Antoine Marteyn, Hubert Löwenheim, Karl‐Heinz Krause, Marcus Müller, Rudolf Glückert, Pascal Senn
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.703489

Reconstruction of the Cytokine Signaling in Lysosomal Storage Diseases by Literature Mining and Network Analysis
Cited by: 3
Author(s): Silvia Parolo, Danilo Tomasoni, Pranami Bora, Alan Ramponi, Chanchala Kaddi, Karim Azer, Enrico Domenici, Susana Neves-Zaph, Rosario Lombardo
Software Mentions: 3
Published: almost 5 years ago

10.1534/g3.119.401031

Loss of N-Glycanase 1 Alters Transcriptional and Translational Regulation in K562 Cell Lines
Cited by: 13
Author(s): William F. Mueller, Petra Jakob, Han Sun, Sandra Clauder‐Münster, Sonja Ghidelli-Disse, Diana Paola Serralde Ordóñez, Markus Böesche, Marcus Bantscheff, Paul Collier, Bettina Haase, Vladimı́r Beneš, Malte Paulsen, Peter Sehr, Joe Lewis, Gerard Drewes, Lars M. Steinmetz
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-23514-z

Comparative transcriptomics gives insights into the evolution of parasitism in Strongyloides nematodes at the genus, subclade and species level
Cited by: 22
Author(s): Vicky L. Hunt, Akinori Hino, Akemi Yoshida, Taisei Kikuchi
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-019-43862-8

CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes
Cited by: 53
Author(s): Alex K. Datsomor, Nikola Zic, Keshuai Li, Rolf Erik Olsen, Yang Jin, Jon Olav Vik, Rolf B. Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge
Software Mentions: 3
Published: about 7 years ago

10.3389/fnins.2012.00156

A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs
Cited by: 13
Author(s): Sergei A. Manakov, Andrew Morton, Anton J. Enright, Seth G. N. Grant
Software Mentions: 3
Published: over 14 years ago

10.1155/2015/140819

MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation
Cited by: 13
Author(s): Luman Wang, Qiaochu Mo, Jianxin Wang
Software Mentions: 3
Published: over 11 years ago

10.3389/fgene.2018.00083

Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned
Cited by: 57
Author(s): Emily Price, Wendy P. Robinson
Software Mentions: 3
Published: about 8 years ago

10.3389/fnmol.2017.00250

Expression and Regulatory Network Analysis of miR-140-3p, a New Potential Serum Biomarker for Autism Spectrum Disorder
Cited by: 25
Author(s): Matilde Cirnigliaro, Cristina Barbagallo, Mariangela Gulisano, Carla Noemi Domini, Rita Barone, Davide Barbagallo, Marco Ragusa, Cinzia Di Pietro, Renata Rizzo, Michele Purrello
Software Mentions: 3
Published: almost 9 years ago

10.3389/fonc.2019.00190

OSlms: A Web Server to Evaluate the Prognostic Value of Genes in Leiomyosarcoma
Cited by: 24
Author(s): Qiang Wang, Longxiang Xie, Yifang Dang, Xiaoxiao Sun, Tiantian Xie, JJ Guo, Yali Han, Zhongyi Yan, Wan Zhu, Yunlong Wang, Wei Li, Xiangqian Guo
Software Mentions: 3
Published: about 7 years ago

10.1038/onc.2015.399

The NF-κB subunit c-Rel regulates Bach2 tumour suppressor expression in B-cell lymphoma
Cited by: 32
Author(s): Jill E. Hunter, Jacqueline Butterworth, Bo Zhao, Hélène Sellier, Kirsteen J. Campbell, Huw D. Thomas, Chris M. Bacon, Simon Cockell, Benjamin E. Gewurz, Neil D. Perkins
Software Mentions: 3
Published: over 10 years ago

10.1515/jib-2018-0080

Gene Expression Studies to Identify Significant Genes in AR, MTOR, MAPK Pathways and their Overlapping Regulatory Role in Prostate Cancer
Cited by: 0
Author(s): Nimisha Asati, Abhinav Mishra, Ayush Shukla, Tiratha Raj Singh
Software Mentions: 3
Published: about 7 years ago

10.3389/fonc.2020.570281

A Three-Metabolic-Genes Risk Score Model Predicts Overall Survival in Clear Cell Renal Cell Carcinoma Patients
Cited by: 8
Author(s): Yiqiao Zhao, Zijia Tao, Xiaonan Chen
Software Mentions: 3
Published: over 5 years ago

10.1111/jipb.13026

Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores
Cited by: 14
Author(s): M. Estrella Santamaría, Alejandro Dorado García, Ana Arnáiz, Irene Rosa‐Diaz, Gara Romero‐Hernandez, Isabel Dı́az, Manuel Martínez
Software Mentions: 3
Published: over 5 years ago

10.1016/j.jhepr.2021.100237

Aramchol downregulates stearoyl CoA-desaturase 1 in hepatic stellate cells to attenuate cellular fibrogenesis
Cited by: 26
Author(s): Dipankar Bhattacharya, Brittany Basta, José M. Mato, Amanda Craig, David Fernández–Ramos, Fernando Lopitz‐Otsoa, Darya Tsvirkun, Liat Hayardeny, Vasuretha Chandar, Robert E. Schwartz, Augusto Villanueva, Scott L. Friedman
Software Mentions: 3
Published: about 5 years ago

10.1007/s00109-012-0925-9

Early steps of microglial activation are directly affected by neuroprotectant FK506 in both in vitro inflammation and in rat model of stroke
Cited by: 33
Author(s): Małgorzata Zawadzka, Michal Dabrowski, Agata Gozdz, Barbara Szadujkis, Marcin Sliwa, Maciej Lipko, Bożena Kamińska
Software Mentions: 3
Published: almost 14 years ago

10.3390/ijms18091900

Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data
Cited by: 3
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 3
Published: almost 9 years ago

10.3389/fendo.2021.628907

Identification of Key Pathways and Genes in Obesity Using Bioinformatics Analysis and Molecular Docking Studies
Cited by: 7
Author(s): Harish Joshi, Basavaraj Vastrad, Nidhi Joshi, Chanabasayya Vastrad, Anandkumar Tengli, Iranna Kotturshetti
Software Mentions: 3
Published: almost 5 years ago

10.1155/2017/2568706

Genomewide Expression and Functional Interactions of Genes under Drought Stress in Maize
Cited by: 34
Author(s): Nepolean Thirunavukkarasu, R.C. Sharma, Nidhi Singh, Kaliyugam Shiriga, Sweta Mohan, Swati Mittal, Mittal Shikha, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta K. Dash, Firoz Hossain, H. S. Gupta
Software Mentions: 3
Published: over 9 years ago

10.3390/jof4030081

Identification of Antifungal Targets Based on Computer Modeling
Cited by: 10
Author(s): Elena Bencúrová, Shishir Gupta, Edita Sarukhanyan, Thomas Dandekar
Software Mentions: 3
Published: almost 8 years ago

10.1038/srep32417

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 20
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Andrew Cowie, Karen Pickard, Massimiliano Mellone, C Choh, Mathieu Derouet, Patrick J. Duriez, Fergus Noble, Michael J. White, John Primrose, Jonathan C. Strefford, Matthew Rose-Zerilli, Gareth J. Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C. Fitzgerald, Tim Underwood
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-017-09490-w

The epigenetic modifier Fam208a is required to maintain epiblast cell fitness
Cited by: 6
Author(s): Shohag Bhargava, Brian Cox, Christiana Polydorou, Veronika Gresakova, Vladimír Kořínek, Hynek Strnad, Radislav Sedláček, Trevor Epp, Kallayanee Chawengsaksophak
Software Mentions: 3
Published: almost 9 years ago

10.7150/jca.38741

Construction and validation of an eight-gene signature with great prognostic value in bladder cancer
Cited by: 13
Author(s): Xin Yan, Xun Fu, Zixin Guo, Xiaoping Li, Tong-Zu Liu, Sheng Li
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1000105

Anti-Fungal Innate Immunity in C. elegans Is Enhanced by Evolutionary Diversification of Antimicrobial Peptides
Cited by: 215
Author(s): Nathalie Pujol, Olivier Zugasti, Daniel Wong, Carole Couillault, C. Léopold Kurz, Hinrich Schulenburg, Jonathan J. Ewbank
Software Mentions: 2
Published: almost 18 years ago

10.3389/fcvm.2019.00165

Single Cell Analysis of Endothelial Cells Identified Organ-Specific Molecular Signatures and Heart-Specific Cell Populations and Molecular Features
Cited by: 64
Author(s): Wei Feng, Lyuqin Chen, Patricia K. Nguyen, Sean M. Wu, Guang Li
Software Mentions: 2
Published: over 6 years ago

10.3389/fcell.2020.629030

Dynamic Expression of m6A Regulators During Multiple Human Tissue Development and Cancers
Cited by: 8
Author(s): Ya Zhang, Sicong Xu, Gang Xu, Yueying Gao, Si Li, Ke Zhang, Zhanyu Tian, Jing Guo, Xia Li, Juan Xu, Yongsheng Li
Software Mentions: 2
Published: over 5 years ago

10.3389/fcell.2020.630492

Human Bile Contains Cholangiocyte Organoid-Initiating Cells Which Expand as Functional Cholangiocytes in Non-canonical Wnt Stimulating Conditions
Cited by: 9
Author(s): Floris J.M. Roos, Monique M A Verstegen, Laura Muñoz Albarinos, Henk P. Roest, Jan‐Werner Poley, G. W. M. Tetteroo, Jan N.M. IJzermans, Luc J. W. van der Laan
Software Mentions: 2
Published: over 5 years ago

10.3389/fcell.2021.642681

Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model Reconstruction
Cited by: 4
Author(s): Þóra Björg Sigmarsdóttir, Sarah McGarrity, James T. Yurkovich, Óttar Rolfsson, Ólafur E. Sigurjónsson
Software Mentions: 2
Published: about 5 years ago

10.3389/fcell.2021.671838

Epigenetic Deregulation of the Histone Methyltransferase KMT5B Contributes to Malignant Transformation in Glioblastoma
Cited by: 6
Author(s): Virginia López, Juan Ramón Tejedor, Antonella Carella, María González García, Pablo Santamarina‐Ojeda, Raúl Fernández Pérez, Cristina Mangas, Rocío G. Urdinguio, A.I. Aranburu, Daniel de la Nava, María D. Corte‐Torres, Aurora Astudillo, Manuela Mollejo, Bárbara Meléndez, Agustín F. Fernández, Mario F. Fraga
Software Mentions: 2
Published: almost 5 years ago

10.3389/fcell.2014.00039

Fingerprints of a message: integrating positional information on the transcriptome
Cited by: 1
Author(s): Erik Dassi, Alessandro Quattrone
Software Mentions: 2
Published: almost 12 years ago

10.3389/fcell.2017.00012

The Importance of REST for Development and Function of Beta Cells
Cited by: 21
Author(s): David Martín, Anne Grapin-Botton
Software Mentions: 2
Published: over 9 years ago

10.3389/fncel.2019.00461

Transcranial Current Stimulation Alters the Expression of Immune-Mediating Genes
Cited by: 20
Author(s): Monika Rabenstein, Marcus Unverricht-Yeboah, Meike Hedwig Keuters, Anton Pikhovych, Joerg Hucklenbroich, Sabine Ulrike Vay, Stefan Blaschke, Anne Ladwig, Henrik Walter, Magdalena Beiderbeck, Gereon R. Fink, Michael Schroeter, Ralf Kriehuber, Maria Adele Rueger
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2021.649764

Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study
Cited by: 1
Author(s): Yesid Cuesta-Astroz, Guilherme Gischkow Rucatti, Leandro Murgas, Carol D. SanMartín, Mario Sanhueza, Alberto J. M. Martin
Software Mentions: 2
Published: almost 5 years ago

10.3389/fgene.2021.625797

Identification of m6A-Associated RNA Binding Proteins Using an Integrative Computational Framework
Cited by: 4
Author(s): Yiqian Zhang, Michiaki Hamada
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.680217

Comparative Genomics Identifies Putative Interspecies Mechanisms Underlying Crbn-Sall4-Linked Thalidomide Embryopathy
Cited by: 1
Author(s): Thayne Woycinck Kowalski, Gabriela Barreto Caldas-Garcia, João Luiz Ellera Gomes, Lucas Rosa Fraga, Lavínia Schüler-Faccini, Mariana Recamonde‐Mendoza, Vanessa Rodrigues Paixão‐Côrtes, Fernanda Sales Luiz Vianna
Software Mentions: 2
Published: almost 5 years ago

10.3389/fgene.2021.646297

Omics Multi-Layers Networks Provide Novel Mechanistic and Functional Insights Into Fat Storage and Lipid Metabolism in Poultry
Cited by: 8
Author(s): Farzad Ghafouri, Abolfazl Bahrami, Mostafa Sadeghi, S. R. Miraei-Ashtiani, Maryam Bakherad, Herman W. Barkema, Samantha Larose
Software Mentions: 2
Published: almost 5 years ago

10.3389/fgene.2018.00108

Identification and Validation of a Diagnostic and Prognostic Multi-Gene Biomarker Panel for Pancreatic Ductal Adenocarcinoma
Cited by: 41
Author(s): Hagen Klett, Hannah Fuellgraf, Ella Levit‐Zerdoun, Saskia Hussung, Silke Kowar, Simon Küsters, Peter Bronsert, Martin Werner, Uwe A. Wittel, Ralph Fritsch, Hauke Busch, Melanie Boerries
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2020.572284

A Transcriptomics-Based Meta-Analysis Combined With Machine Learning Identifies a Secretory Biomarker Panel for Diagnosis of Pancreatic Adenocarcinoma
Cited by: 13
Author(s): Indu Khatri, Manoj Bhasin
Software Mentions: 2
Published: almost 6 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Penalties:

Papers Mentioning ArrayExpress 1,962