bioconductor: ArrayExpress | Projects

10.1186/gb-2008-9-10-r146

A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection
Cited by: 19
Author(s): Amanda Greenall, Guiyuan Lei, Daniel Swan, Katherine James, Liming Wang, Heiko Peters, Anil Wipat, Darren J. Wilkinson, David Lydall
Software Mentions: 3
Published: about 18 years ago

10.1186/gb-2012-13-4-r31

Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel
Cited by: 33
Author(s): Marieke Simonis, Santosh S. Atanur, Sam E.V. Linsen, Victor Guryev, Frans-Paul Ruzius, Laurence Gamé, Nico Lansu, Ewart de Bruijn, Sebastiaan van Heesch, Steven J.M. Jones, Michal Pravenec, Tim Aitman, Edwin Cuppen
Software Mentions: 3
Published: about 14 years ago

10.1186/1471-2105-13-85

DIPSBC - data integration platform for systems biology collaborations
Cited by: 13
Author(s): Felix Dreher, Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, K. Schellander, Hans Lehrach, Bodo Lange, Ralf Herwig
Software Mentions: 3
Published: almost 14 years ago

10.1186/1471-2164-10-98

SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip® expression data
Cited by: 26
Author(s): Adriane Menßen, Götz Edinger, Joachim R. Grün, Ulrike Haase, Ria Baumgrass, Andreas Grützkau, Andreas Radbruch, G.-R. Burmester, Thomas Häupl
Software Mentions: 3
Published: about 17 years ago

10.1186/s12943-020-01155-z

Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme
Cited by: 57
Author(s): Mathilde Cheray, Amandine Etcheverry, Camille Jacques, Romain Pacaud, Gwenola Bougras-Cartron, Marc Aubry, Florent Denoual, Pierre Peterlongo, Arulraj Nadaradjane, Joséphine Briand, Farida Akcha, Dominique Heymann, François M. Vallette, Jean Mosser, Benjamin Ory, Pierre-François Cartron
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2164-14-127

Genetic analysis of the Trichuris muris-induced model of colitis reveals QTL overlap and a novel gene cluster for establishing colonic inflammation
Cited by: 20
Author(s): Scott Levison, Paul Fisher, Jenny Hankinson, Leo Zeef, Steve Eyre, William Ollier, John McLaughlin, Andy Brass, Richard K. Grencis, Joanne L. Pennock
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12943-016-0554-y

Systems analysis identifies miR-29b regulation of invasiveness in melanoma
Cited by: 18
Author(s): Miles C. Andrews, Joseph Cursons, Daniel Hurley, Matthew Anaka, Jonathan Cebon, Andreas Behren, Edmund J. Crampin
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0226707

High expression of olfactomedin-4 is correlated with chemoresistance and poor prognosis in pancreatic cancer
Cited by: 15
Author(s): Ryotaro Ohkuma, Erica Yada, Shumpei Ishikawa, Daisuke Komura, Hidenobu Ishizaki, Koji Tamada, Yutaro Kubota, Kazuyuki Hamada, Hiroo Ishida, Yuya Hirasawa, Hirotsugu Ariizumi, Etsuko Satoh, Midori Shida, Makoto Watanabe, Rie Onoue, Kiyohiro Ando, Junji Tsurutani, Kiyoshi Yoshimura, Takehiko Yokobori, Tetsuro Sasada, Takeshi Aoki, Masahiko Murakami, Tomoko Norose, Nobuyuki Ohike, Masafumi Takimoto, Masahiko Izumizaki, Shinichi Kobayashi, Takuya Tsunoda, Satoshi Wada
Software Mentions: 3
Published: about 6 years ago

10.1186/gb-2013-14-10-r110

Modeling precision treatment of breast cancer
Cited by: 263
Author(s): Anneleen Daemen, Obi L. Griffith, Laura M. Heiser, Nicholas J. Wang, Oana Enache, Zachary Sanborn, François Pépin, Steffen Durinck, James E. Korkola, Malachi Griffith, Joe S. Hur, Nam Huh, Jongsuk Chung, Leslie Cope, Mary Jo Fackler, Christopher B. Umbricht, Saraswati Sukumar, Pankaj Seth, Vikas P. Sukhatme, Lakshmi R. Jakkula, Yiling Lu, Gordon B. Mills, Raymond J. Cho, Eric A. Collisson, Laura J. van’t Veer, Paul T. Spellman, Joe W. Gray
Software Mentions: 3
Published: about 13 years ago

10.3389/fbioe.2020.584614

Revisiting the Growth Modulon of Corynebacterium glutamicum Under Glucose Limited Chemostat Conditions
Cited by: 5
Author(s): Michaela Graf, Thorsten Haas, Attila Teleki, André Feith, Martin Cerff, Wolfgang Wiechert, Katharina Nöh, Tobias Busche, Jörn Kalinowski, Ralf Takors
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-15-S14-S4

linkedISA: semantic representation of ISA-Tab experimental metadata
Cited by: 55
Author(s): Alejandra N. González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0115911

The Transcriptomic and Proteomic Landscapes of Bone Marrow and Secondary Lymphoid Tissues
Cited by: 14
Author(s): Sandra Andersson, Kenneth Nilsson, Linn Fagerberg, Björn M. Hallström, Christer Sundström, Anna Danielsson, Karolina Edlund, Mathias Uhlén, Anna Asplund
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0078868

Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets
Cited by: 4
Author(s): Wensheng Zhang, Andrea Edwards, Erik K. Flemington, Kun Zhang
Software Mentions: 3
Published: over 12 years ago

10.12688/f1000research.10960.2

A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification
Cited by: 11
Author(s): Jessica Roelands, Julie Decock, Sabri Boughorbel, Darawan Rinchai, Cristina Maccalli, Michele Ceccarelli, Michael A. Black, Chris Print, Jeff Chou, Scott Presnell, Charlie Quinn, Puthen V. Jithesh, Najeeb Syed, Salha B.J. Al Bader, Shahinaz Bedri, Ena Wang, Francesco M. Marincola, Damien Chaussabel, Peter J.K. Kuppen, Lance D. Miller, Davide Bedognetti, Wouter Hendrickx
Software Mentions: 3
Published: about 8 years ago

10.12688/f1000research.9611.3

Revisiting inconsistency in large pharmacogenomic studies
Cited by: 42
Author(s): Zhaleh Safikhani, Петр Смирнов, Mark Freeman, Nehmé El-Hachem, Adrian She, Rene Quevedo, Anna Goldenberg, Nicolai J. Birkbak, Christos Hatzis, Leming Shi, Andrew H. Beck, Hugo J.W.L. Aerts, John Quackenbush, Benjamin Haibe‐Kains
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0234299

Yellow sea mediated segregation between North East Asian Dryophytes species
Cited by: 18
Author(s): Amaël Borzée, Kevin R. Messenger, Shinhyeok Chae, Desiree Andersen, Jordy Groffen, Ye Inn Kim, Junghwa An, Siti N. Othman, Kyongsin Ri, Tu Yong Nam, Yoonhyuk Bae, Jin Ren, Jia Tang Li, Ming‐Feng Chuang, Yoonjung Yi, Yucheol Shin, Taejoon Kwon, Yikweon Jang, Mi Sook Min
Software Mentions: 3
Published: over 5 years ago

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: about 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: almost 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: almost 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: almost 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: over 8 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: about 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: about 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: almost 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: about 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: over 6 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: about 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: over 11 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: about 13 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: over 7 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: over 5 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: over 13 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: about 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: about 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: almost 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: about 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: about 18 years ago

10.1186/1476-4598-9-189

The dietary isothiocyanate sulforaphane modulates gene expression and alternative gene splicing in a PTEN null preclinical murine model of prostate cancer
Cited by: 50
Author(s): Μαρία Τράκα, Caroline A Spinks, Joanne F. Doleman, Antonietta Melchini, Richard Y. Ball, Robert Mills, Richard Mithen
Software Mentions: 3
Published: over 15 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: about 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: about 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: about 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: over 6 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: over 6 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: over 14 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: over 10 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: about 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: about 11 years ago

10.1016/j.mce.2020.111007

Hypoxia regulates GR function through multiple mechanisms involving microRNAs 103 and 107
Cited by: 11
Author(s): Nan Yang, Andrew Berry, Carolin M Sauer, Matthew Baxter, Ian J. Donaldson, Karen Forbes, Rachelle Donn, Laura Matthews, David Ray
Software Mentions: 3
Published: about 5 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/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: almost 7 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

10.3389/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: over 4 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: almost 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: over 7 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: over 6 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: about 14 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: almost 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: about 5 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: almost 8 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: almost 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: about 14 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: over 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: almost 8 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: about 6 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: over 4 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: almost 6 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: over 6 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: about 8 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/s41598-017-09490-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: over 8 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: almost 7 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: over 7 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: 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

10.1038/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: over 9 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: almost 5 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: almost 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: over 8 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

10.3389/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: about 5 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: almost 7 years ago

10.3389/fmicb.2017.02676

Transcriptional Modulation of Penicillin-Binding Protein 1b, Outer Membrane Protein P2 and Efflux Pump (AcrAB-TolC) during Heat Stress Is Correlated to Enhanced Bactericidal Action of Imipenem on Non-typeable Haemophilus influenzae
Cited by: 3
Author(s): Abdessalam Cherkaoui, Seydina M. Diène, Adrien Fischer, Stefano Leo, Patrice François, Jacques Schrenzel
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2017.01556

Transcriptomic Analyses Reveal Differential Gene Expression of Immune and Cell Death Pathways in the Brains of Mice Infected with West Nile Virus and Chikungunya Virus
Cited by: 21
Author(s): Stephanie M. Lim, Henk-Jan van den Ham, Minoushka Oduber, Eurydice Martina, Fatiha Zaaraoui-Boutahar, Jeroen M. Roose, Wilfred F. J. van IJcken, Albert D. M. E. Osterhaus, Arno C. Andeweg, Penelope Koraka, Byron Martina
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2020.01314

Network-Based Analysis of OMICs Data to Understand the HIV–Host Interaction
Cited by: 13
Author(s): Sergey Ivanov, Alexey Lagunin, Dmitry Filimonov, O. Tarasova
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2018.01955

Active HHV-6 Infection of Cerebellar Purkinje Cells in Mood Disorders
Cited by: 41
Author(s): Bhupesh K. Prusty, Nitish Gulve, Sheila Govind, G. R. F. Krueger, Julia Feichtinger, Lee Larcombe, Richard Aspinall, Dharam V. Ablashi, Carla Toro
Software Mentions: 2
Published: over 7 years ago

10.3389/fmolb.2021.567730

A Novel Nine Apoptosis-Related Genes Signature Predicting Overall Survival for Kidney Renal Clear Cell Carcinoma and its Associations with Immune Infiltration
Cited by: 13
Author(s): Yi Wang, Yinhao Chen, Bingye Zhu
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-019-44235-x

Cynomolgus macaque IL37 polymorphism and control of SIV infection
Cited by: 3
Author(s): Takashi Shiina, Shingo Suzuki, Nicolas Congy-Jolivet, Alice Aarnink, Henri‐Jean Garchon, Nathalie Dereuddre‐Bosquet, Bruno Vaslin, Nicolas Tchitchek, Delphine Desjardins, Brigitte Autran, Olivier Lambotte, Ioannis Théodorou, Roger Le Grand, Antoine Blancher
Software Mentions: 2
Published: over 6 years ago

10.3389/fnana.2016.00086

HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development
Cited by: 63
Author(s): Susan Lindsay, Yaobo Xu, Steven Lisgo, Lauren F. Harkin, Andrew J. Copp, Dianne Gerrelli, Gavin J. Clowry, Aysha Talbot, Michael J. Keogh, Jonathan Coxhead, Mauro Santibanez‐Koref, Patrick F. Chinnery
Software Mentions: 2
Published: over 9 years ago

10.3389/fgene.2020.626536

Characterization of Genome-Wide DNA Methylation and Hydroxymethylation in Mouse Arcuate Nucleus of Hypothalamus During Puberty Process
Cited by: 13
Author(s): Yihang Shen, Shasha Zhou, Xiaodong Zhao, Hua Li, Jingyong Sun
Software Mentions: 2
Published: about 5 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: over 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: almost 8 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: over 4 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: over 4 years ago

10.3389/fonc.2020.00645

Protective Role of Decorin in Primary Hepatocellular Carcinoma
Cited by: 19
Author(s): Andrea Reszegi, Zsolt Horváth, Hajnalka Fehér, Barnabás Wichmann, Péter Tátrai, Ilona Kovalszky, Kornélia Baghy
Software Mentions: 2
Published: almost 6 years ago

10.3389/fphar.2019.00561

In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR
Cited by: 53
Author(s): Gopal Pawar, Judith C. Madden, David J. Ebbrell, James W. Firman, Mark T.D. Cronin
Software Mentions: 2
Published: over 6 years ago

10.3389/fphys.2017.00253

Identification, Classification, and Expression Analysis of GRAS Gene Family in Malus domestica
Cited by: 41
Author(s): Shiliang Fan, Dong Zhang, Giampiero Cai, Ming Zhao, Haiqin Wu, Youmei Li, Yongming Shen, Mingyu Han
Software Mentions: 2
Published: almost 9 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962