bioconductor: ArrayExpress | Projects

10.1186/1756-0500-6-72

The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization
Cited by: 2
Author(s): Jaishree Garhyan, Raad Z. Gharaibeh, Stephen J. McGee, Cynthia Gibas
Software Mentions: 2
Published: over 13 years ago

10.1186/1756-0500-4-157

Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation
Cited by: 10
Author(s): Robab Hakim-Weber, Anne Krogsdam, Claus Jørgensen, Maria Fischer, Andreas Prokesch, Juliane Gertrude Bogner‐Strauß, Stefan R. Bornstein, Jacob B. Hansen, Lise Madsen, Karsten Kristiansen, Zlatko Trajanoski, Hubert Hackl
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0181365

Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice
Cited by: 6
Author(s): Olusegun Oshota, Max Conway, María Fookes, Fernanda Schreiber, Roy R. Chaudhuri, Lu Yu, Fiona J. E. Morgan, Simon Clare, Jyoti S. Choudhary, Nicholas R. Thomson, Píetro Lió, Duncan J. Maskell, Pietro Mastroeni, A. Grant
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1000663

Imprinting of the Polycomb Group Gene MEDEA Serves as a Ploidy Sensor in Arabidopsis
Cited by: 137
Author(s): Aleksandra Erilova, Lynette Brownfield, Vivien Exner, Marisa Rosa, David Twell, Ortrun Mittelsten Scheid, Lars Hennig, Claudia Köhler
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0004128

Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments
Cited by: 26
Author(s): Luca Beltrame, Lisa Rizzetto, Raffaele Paola, Philippe Rocca-Serra, Luca Gambineri, Cristina Battaglia, Duccio Cavalieri
Software Mentions: 2
Published: over 17 years ago

10.1530/ERC-14-0454

HES5 silencing is an early and recurrent change in prostate tumourigenesis
Cited by: 10
Author(s): Charles E. Massie, Inmaculada Spiteri, Helen Ross-Adams, Hayley J. Luxton, Jonathan Kay, Hayley C. Whitaker, Mark J. Dunning, Alastair Lamb, Antonio Ramos-Montoya, Daniel Brewer, Christopher S. Cooper, Rosalind Eeles, _ _, Anne Y. Warren, Simon Tavaré, David E. Neal, Andy G. Lynch
Software Mentions: 2
Published: over 11 years ago

10.1111/1462-2920.13930

Transcriptome and proteome dynamics in chemostat culture reveal how<i>Campylobacter jejuni</i>modulates metabolism, stress responses and virulence factors upon changes in oxygen availability
Cited by: 28
Author(s): Edward Guccione, John J. Kendall, Andrew Hitchcock, Nitanshu Garg, Michael A. White, Francis Mulholland, Robert K. Poole, David J. Kelly
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.33506

Epidermal LysM receptor ensures robust symbiotic signalling in Lotus japonicus
Cited by: 48
Author(s): Eiichi Murakami, Jeryl Cheng, Kira Gysel, Zoltán Bozsóki, Yasuyuki Kawaharada, Christian T. Hjuler, Kasper K. Sørensen, Ke Tao, Simon Kelly, Francesco Venice, Andrea Genre, Mikkel B. Thygesen, Noor de Jong, Maria Vinther, Dorthe Bødker Jensen, Knud J. Jensen, Mickaël Blaise, Lene Heegaard Madsen, Kasper R. Andersen, Jens Stougaard, Simona Radutoiu
Software Mentions: 2
Published: almost 8 years ago

10.1038/onc.2015.526

A RelA(p65) Thr505 phospho-site mutation reveals an important mechanism regulating NF-κB-dependent liver regeneration and cancer
Cited by: 28
Author(s): Anna Moles, Jacqueline Butterworth, Ana M. Sánchez, Jill E. Hunter, Jack Leslie, Hélène Sellier, Dina Tiniakos, Simon Cockell, Derek A. Mann, Fiona Oakley, Neil D. Perkins
Software Mentions: 2
Published: over 10 years ago

10.1007/s11356-017-0515-z

Transcriptional changes measured in rice roots after exposure to arsenite-contaminated sediments
Cited by: 7
Author(s): Alexandra Brinke, Georg Reifferscheid, Roland Klein, Ute Feiler, Sebastian Buchinger
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-9-266

Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus
Cited by: 100
Author(s): Jennifer Owen, B Ann Hedley, Claus Svendsen, Jodie F Wren, Martijs J. Jonker, Peter K. Hankard, Linsey J Lister, Stephen R. Stürzenbaum, Andrew Morgan, David J. Spurgeon, Mark Blaxter, Peter Kille
Software Mentions: 2
Published: about 18 years ago

10.1186/s13072-018-0232-y

Non-canonical Drosophila X chromosome dosage compensation and repressive topologically associated domains
Cited by: 7
Author(s): Hangnoh Lee, Brian Oliver
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1002505

Coexpression Network Analysis in Abdominal and Gluteal Adipose Tissue Reveals Regulatory Genetic Loci for Metabolic Syndrome and Related Phenotypes
Cited by: 56
Author(s): Josine L. Min, George Nicholson, Ingileif Halgrimsdottir, Kristian Almstrup, Andreas Petri, Amy Barrett, Mary E. Travers, Nigel W. Rayner, Reedik Mägi, Fredrik Pettersson, John Broxholme, Matt J. Neville, Quin F. Wills, Jane Cheeseman, Maxine Allen, Chris Holmes, Tim D. Spector, Jan Fleckner, Mark I. McCarthy, Fredrik Karpe, Cecilia M. Lindgren, Krina T. Zondervan
Software Mentions: 2
Published: over 14 years ago

10.26508/lsa.201900356

Oxidised metabolites of the omega-6 fatty acid linoleic acid activate dFOXO
Cited by: 15
Author(s): So Yeon Kwon, Karen A. Massey, Mark A. Watson, Tayab Hussain, Giacomo Volpe, Christopher D. Buckley, Anna Nicolaou, Paul Badenhorst
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0229536

Identification of trypanosomatids and blood feeding preferences of phlebotomine sand fly species common in Sicily, Southern Italy
Cited by: 30
Author(s): Jessica Maria Abbate, Carla Maia, André Pereira, Francesca Arfuso, Gabriella Gaglio, Maria Rizzo, Giulia Caracappa, Gabriele Marino, Matthias Pollmeier, S. Giannetto, Emanuele Brianti
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0242874

Interaction of preimplantation factor with the global bovine endometrial transcriptome
Cited by: 3
Author(s): Ruth Wonfor, Christopher J. Creevey, Manuela Natoli, Matthew J. Hegarty, Deborah Nash, Michael T. Rose
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0044800

Mining Gene Expression Signature for the Detection of Pre-Malignant Melanocytes and Early Melanomas with Risk for Metastasis
Cited by: 21
Author(s): Cláudia Souza, Patrícia Xander, Ana Carolina Monteiro, Amanda Gonçalves dos Santos Silva, Débora Castanheira Pereira da Silva, Sabine Mai, Viviane Bernardo, José Daniel Lopes, Miriam Galvonas Jasiulionis
Software Mentions: 2
Published: almost 14 years ago

10.1186/s40001-018-0328-7

Membrane-bound estrogen receptor alpha initiated signaling is dynamin dependent in breast cancer cells
Cited by: 9
Author(s): István Marczell, Petra Balogh, G Nyírő, Anna L. Kiss, Balázs Kovács, Gábor Békési, Kàroly Rácz, Attila Patócs
Software Mentions: 2
Published: about 8 years ago

10.1186/1753-6561-5-S2-S10

Managing and querying gene expression data using Curray
Cited by: 3
Author(s): Hasan M. Jamil, Aminul Islam
Software Mentions: 2
Published: about 15 years ago

10.1186/1471-2164-14-82

DNA methylation profile dynamics of tissue-dependent and differentially methylated regions during mouse brain development
Cited by: 15
Author(s): Keiji Hirabayashi, Kunio Shiota, Shusuke Yagi
Software Mentions: 2
Published: over 13 years ago

10.1038/s41388-018-0588-2

LCE: an open web portal to explore gene expression and clinical associations in lung cancer
Cited by: 70
Author(s): Ling Cai, Shing-Jong Lin, Luc Girard, Yunyun Zhou, Lin Yang, Bo Ci, Qinbo Zhou, Danni Luo, Bo Yao, Jing Tang, Jeffrey D. Allen, Kenneth E. Huffman, Adi F. Gazdar, John V. Heymach, Ignacio I. Wistuba, Guanghua Xiao, John D. Minna, Yang Xie
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-13-620

MMpred: functional miRNA – mRNA interaction analyses by miRNA expression prediction
Cited by: 10
Author(s): Przemyslaw Stempor, Michael Cauchi, P. David Wilson
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0233818

Intracellular Cryptococcus neoformans disrupts the transcriptome profile of M1- and M2-polarized host macrophages
Cited by: 16
Author(s): Aarthi Subramani, Prianca Griggs, Niah Frantzen, James Mendez, Jamila S Tucker, Jada Murriel, Linda M. Sircy, Grace E. Millican, Erin E. McClelland, Rebecca L. Seipelt-Thiemann, David E. Nelson
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0235401

Antimalarial drug resistance molecular makers of Plasmodium falciparum isolates from Sudan during 2015–2017
Cited by: 13
Author(s): Maazza Hussien, Muzamil Mahdi Abdel Hamid, Elamin Abdelkarim Elamin, Abdalla O. Hassan, Arwa Elaagip, Abusofyan Hamattallah A. Salama, Mohammed H. Abdelraheem, Abdelrahim Mohamed
Software Mentions: 2
Published: almost 6 years ago

10.3390/metabo8040084

An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction
Cited by: 12
Author(s): Amornpan Klanchui, Sudarat Dulsawat, Kullapat Chaloemngam, Supapon Cheevadhanarak, Peerada Prommeenate, Asawin Meechai
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-10-214

Construction and use of gene expression covariation matrix
Cited by: 3
Author(s): Jérôme Hennetin, Petri Pehkonen, Michel Bellis
Software Mentions: 2
Published: almost 17 years ago

10.18632/oncotarget.23973

Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer
Cited by: 15
Author(s): Debashis Sahoo, Wei Wei, Heidi Auman, Antonio Hurtado-Coll, Peter R. Carroll, Ladan Fazli, Martin Gleave, Daniel W. Lin, Peter S. Nelson, Jeff Simko, Ian M. Thompson, Robin J. Leach, Dean A. Troyer, Lawrence D. True, Jesse K. McKenney, Ziding Feng, James D. Brooks
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-018-5336-z

Characterization of B-BOX gene family and their expression profiles under hormonal, abiotic and metal stresses in Poaceae plants
Cited by: 48
Author(s): Abdullah Shalmani, Xiu-Qing Jing, Yi Shi, Izhar Muhammad, Meng-Ru Zhou, Xiaoli Wei, Qiongqiong Chen, Wenqiang Li, Wenting Liu, Kun-Ming Chen
Software Mentions: 2
Published: over 7 years ago

10.1007/s11306-015-0810-y

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access
Cited by: 122
Author(s): Reza M. Salek, Steffen Neumann, Daniel Schober, Jan Hummel, Kenny Billiau, Joachim Kopka, Elon Correa, Theo H. Reijmers, Antonio Rosato, Leonardo Tenori, Paola Turano, Silvia Marín, Catherine Deborde, Daniel Jacob, Dominique Rolin, Benjamin Dartigues, Pablo Conesa, Kenneth Haug, Philippe Rocca-Serra, Steve O’Hagan, Jie Hao, Michael Van Vliet, Marko Sysi-Aho, Christian Ludwig, Jildau Bouwman, Marta Cascante, Timothy M. D. Ebbels, Julian L. Griffin, Annick Moing, Macha Nikolski, Matej Orešič, Susanna-Assunta Sansone, Mark R. Viant, Royston Goodacre, Ulrich L. Günther, Thomas Hankemeier, Claudio Luchinat, Dirk Walther, Christoph Steinbeck
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0249432

PAH-pollution effects on sensitive and resistant embryos: Integrating structure and function with gene expression
Cited by: 4
Author(s): Goran Bozinovic, Damian Shea, Zuying Feng, David E. Hinton, Tim L. Sit, Marjorie F. Oleksiak
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1005251

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding
Cited by: 34
Author(s): Xin Xie, Michael J. T. Stubbington, Jesper K. Nissen, Kristian G. Andersen, Daniel Hebenstreit, Sarah A. Teichmann, Alexander G. Betz
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-14-436

Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules
Cited by: 15
Author(s): Katrina Williams, William A Bryant, Victoria A Jenkins, Geraint Barton, Adam A. Witney, John W. Pinney, Brian D. Robertson
Software Mentions: 2
Published: almost 13 years ago

10.12688/f1000research.28449.1

Recommendations for the FAIRification of genomic track metadata
Cited by: 7
Author(s): Sveinung Gundersen, Sanjay Boddu, Salvador Capella-Gutierrez, Finn Drabløs, José Marı́a Fernández, Radmila Kompova, Kieron Taylor, Dmytro Titov, Daniel R. Zerbino, Eivind Hovig
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0244056

Viruses in unexplained encephalitis cases in American black bears (Ursus americanus)
Cited by: 10
Author(s): Charles E. Alex, Elizabeth Fahsbender, Eda Altan, Robert J. Bildfell, Peregrine L. Wolff, Ling Jin, Wendy Black, K. A. Jackson, Leslie W. Woods, Brandon Munk, Tiffany Tse, Eric Delwart, Patricia A. Pesavento
Software Mentions: 2
Published: over 5 years ago

10.12688/f1000research.15119.1

Norwegian e-Infrastructure for Life Sciences (NeLS)
Cited by: 10
Author(s): Kidane Tekle, Sveinung Gundersen, Kjetil Klepper, Lars Ailo Bongo, Inge Alexander Raknes, Xiaxi Li, Zhang Wei, Christian Andreetta, Teshome Dagne Mulugeta, Matúš Kalaš, Morten Rye, Erik Hjerde, Jeevan Karloss Antony Samy, Ghislain Fornous, Abdulrahman Azab, Dag Inge Våge, Eivind Hovig, Nils Peder Willassen, Finn Drabløs, Ståle Nygård, Kjell Petersen, Inge Jonassen
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2164-14-297

Genome-wide analysis of the GH3 family in apple (Malus × domestica)
Cited by: 65
Author(s): Hao Yuan, Kai Zhao, Hengjiu Lei, Xinjie Shen, Yun Liu, Xiudong Liao, Tianhong Li
Software Mentions: 2
Published: about 13 years ago

10.1098/rsob.190299

Molecular anatomy of the pre-primitive-streak chick embryo
Cited by: 17
Author(s): Hyung Chul Lee, Hui-Chun Lu, Mark Turmaine, Nidia M M Oliveira, Youwen Yang, Irene De Almeida, Claudio D. Stern
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-7-145

Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis
Cited by: 44
Author(s): Ella Palmer, Andrew D. Miller, Tom C. Freeman
Software Mentions: 2
Published: about 20 years ago

10.3390/ijms20194740

The CXCR4–CXCL12-Axis Is of Prognostic Relevance in DLBCL and Its Antagonists Exert Pro-Apoptotic Effects In Vitro
Cited by: 13
Author(s): Katrin Pansy, Julia Feichtinger, Barbara Ehall, Barbara Uhl, Miriam Sedej, David Roula, Beata Pursche, Axel Wolf, Manuel Zoidl, Elisabeth Steinbauer, Verena Gruber, Hildegard Greinix, Katharina Prochazka, Gerhard G. Thallinger, Ákos Heinemann, Christine Beham–Schmid, Peter Neumeister, Tanja Wrodnigg, Karoline Fechter, Alexander Deutsch
Software Mentions: 2
Published: over 6 years ago

10.1186/s13229-017-0136-x

Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder—implications of a copy number variation involving DPP10
Cited by: 12
Author(s): A. Mak, Annie Ting Gee Chiu, Gordon Leung, Christopher Chun Yu Mak, Yoyo Wing Yiu Chu, Gary Tsz Kin Mok, Wing Fai Tang, Kelvin Y.K. Chan, Mary Hoi Yin Tang, Elizabeth Tak-Kwong Lau Yim, Kin Wai So, Victoria Qinchen Tao, Cheuk Wing Fung, Virginia Wong, Mohammed Uddin, So Lun Lee, Christian R. Marshall, Stephen W. Scherer, Anita Sik Yau Kan, Brian Hon Yin Chung
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2164-13-187

Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit
Cited by: 32
Author(s): Viviana Lima-Silva, Abel Rosado, Vítor Amorim‐Silva, Antonio Muñoz‐Mérida, Clara Pons, Aureliano Bombarely, Oswaldo Trelles, Rafael Fernández-Muñoz, Antonio Granell, Victoriano Valpuesta, Miguel A. Botella
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-12-262

GiSAO.db: a database for ageing research
Cited by: 3
Author(s): Edith Hofer, Gerhard Laschober, Matthias Hackl, Gerhard G. Thallinger, Günter Lepperdinger, Johannes Grillari, Pidder Jansen‐Dürr, Zlatko Trajanoski
Software Mentions: 2
Published: about 15 years ago

10.1093/molbev/msu226

Transcript Length Mediates Developmental Timing of Gene Expression Across Drosophila
Cited by: 51
Author(s): Carlo G. Artieri, Hunter B. Fraser
Software Mentions: 2
Published: almost 12 years ago

10.1111/febs.15261

Data libraries – the missing element for modeling biological systems
Cited by: 3
Author(s): Anastasia Baryshnikova
Software Mentions: 2
Published: over 6 years ago

10.1002/2211-5463.12354

The clinical value of miR-193a-3p in non-small cell lung cancer and its potential molecular mechanism explored<i>in silico</i>using RNA-sequencing and microarray data
Cited by: 11
Author(s): Xiang Gao, Rongjiang Tang, Qiongni Xie, Jiaying Lin, Hong-lan Shi, Gang Chen, Zu‐Yun Li
Software Mentions: 2
Published: over 8 years ago

10.1186/1476-4598-10-29

miR-449 inhibits cell proliferation and is down-regulated in gastric cancer
Cited by: 199
Author(s): Tony Bou Kheir, Ewa Futoma-Kazmierczak, Anders Jacobsen, Anders Krogh, Linda Bardram, Christoffer Hother, Kirsten Grønbæk, Birgitte Federspiel, Anders H. Lund, Lennart Friis‐Hansen
Software Mentions: 2
Published: about 15 years ago

10.1186/1476-4598-7-6

Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile
Cited by: 69
Author(s): Ingrid Cifola, Roberta Spinelli, Luca Beltrame, Clelia Peano, Ester Fasoli, Stefano Ferrero, Silvano Bòsari, Stefano Signorini, Francesco Rocco, R Perego, Vanessa Proserpio, Francesca Raimondo, Paolo Mocarelli, Cristina Battaglia
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pone.0237245

Increasing temperature can modify the effect of straw mulching on soil C fractions, soil respiration, and microbial community composition
Cited by: 10
Author(s): Xin Fu, Jun Wang, Meng-Yi Xie, Fazhu Zhao, Russell Doughty
Software Mentions: 2
Published: almost 6 years ago

10.1186/1476-4598-9-115

Determination of genes and microRNAs involved in the resistance to fludarabine in vivo in chronic lymphocytic leukemia
Cited by: 73
Author(s): Etienne Moussay, Valérie Palissot, Laurent Vallar, Hélène Poirel, Thomas Wenner, Victoria El Khoury, Nasséra Aouali, Kris Van Moer, Bernadette Leners, François Bernardin, Arnaud Muller, Pascale Cornillet‐Lefèbvre, Alain Delmer, Caroline Duhem, F. Ries, Eric Van Dyck, Guy Berchem
Software Mentions: 2
Published: over 16 years ago

10.1186/1476-4598-12-130

miR-125b targets erythropoietin and its receptor and their expression correlates with metastatic potential and ERBB2/HER2 expression
Cited by: 74
Author(s): Manuela Ferracin, Cristian Bassi, Massimo Pedriali, Sara Pagotto, Lucilla D’Abundo, Barbara Zagatti, Fabio Corrà, Gentian Musa, Elisa Callegari, Laura Lupini, Stefano Volpato, Patrizia Querzoli, Massimo Negrini
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0225873

Dual oxidase Duox and Toll-like receptor 3 TLR3 in the Toll pathway suppress zoonotic pathogens through regulating the intestinal bacterial community homeostasis in Hermetia illucens L.
Cited by: 17
Author(s): Yaqing Huang, Yongqiang Yu, Shuai Zhan, Jeffery K. Tomberlin, Dian Huang, Minmin Cai, Longyu Zheng, Yu Zhou, Jibin Zhang
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2164-10-619

The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes
Cited by: 6
Author(s): Fernando Cruz, Julien Roux, Marc Robinson‐Rechavi
Software Mentions: 2
Published: over 17 years ago

10.3389/fbioe.2019.00106

Cyberbiosecurity Challenges of Pathogen Genome Databases
Cited by: 15
Author(s): Boris A. Vinatzer, Lenwood S. Heath, Hussain M. J. Almohri, Michael J. Stulberg, Christopher J. Lowe, Song Li
Software Mentions: 2
Published: about 7 years ago

10.1128/mSystems.00014-16

OsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping Regulons
Cited by: 28
Author(s): Mia Urem, Teunke van Rossum, Giselda Bucca, Geri F. Moolenaar, Emma Laing, Magda A. Świątek-Połatyńska, Joost Willemse, Elodie Tenconi, Sébastien Rigali, Nora Goosen, Colin P. Smith, Gilles P. van Wezel
Software Mentions: 2
Published: almost 10 years ago

10.1093/pcp/pct178

ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants
Cited by: 92
Author(s): Takeshi Obayashi, Yasunobu Okamura, Satoshi Ito, Shu Tadaka, Yosuke Aoki, Matsuyuki Shirota, Kengo Kinoshita
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0121042

Host Glycan Sugar-Specific Pathways in Streptococcus pneumonia: Galactose as a Key Sugar in Colonisation and Infection
Cited by: 67
Author(s): Laura Paixão, J.Santos Oliveira, André Veríssimo, Susana Vinga, Eva C. Lourenço, M. Rita Ventura, Morten Kjos, Jan‐Willem Veening, Vitor E. Fernandes, Peter W. Andrew, Hasan Yeşilkaya, Ana Rute Neves
Software Mentions: 2
Published: about 11 years ago

10.1186/s12943-020-01217-2

LINC00173.v1 promotes angiogenesis and progression of lung squamous cell carcinoma by sponging miR-511-5p to regulate VEGFA expression
Cited by: 85
Author(s): Jia‐Rong Chen, Aibin Liu, Zhihui Wang, Bin Wang, Xingxing Chai, Wenjie Lu, Ting Cao, Ronggang Li, Mingyan Wu, Zhuming Lu, Wei Pang, Lin Xiao, Xiangmeng Chen, Yan Zheng, Qiong Chen, Jincheng Zeng, Jun Li, Xin Zhang, Dong Ren, Yanming Huang
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2164-8-452

Gene expression analysis reveals early changes in several molecular pathways in cerebral malaria-susceptible mice versus cerebral malaria-resistant mice
Cited by: 55
Author(s): Nicolas Nf Delahaye, Nicolas Coltel, Denis Puthier, Mathieu Barbier, P. Benech, Florence Joly, Fuad Fa Iraqi, Georges E. Grau, Catherine Nguyen, Pascal Rihet
Software Mentions: 2
Published: over 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

10.1186/s12864-016-2600-y

Gene expression comparison of resistant and susceptible Atlantic salmon fry challenged with Infectious Pancreatic Necrosis virus reveals a marked contrast in immune response
Cited by: 53
Author(s): Diego Robledo, John B. Taggart, J. Ireland, Brendan McAndrew, W. Starkey, Chris Haley, Alastair Hamilton, D. R. Guy, J. C. Mota-Velasco, Almas Gheyas, A. E. Tinch, David W. Verner–Jeffreys, Richard Paley, Georgina S. E. Rimmer, I. Tew, Stephen Bishop, James E. Bron, Ross D. Houston
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0106479

De-Novo Learning of Genome-Scale Regulatory Networks in S. cerevisiae
Cited by: 19
Author(s): Sisi Ma, Patrick Kemmeren, David Gresham, Alexander Statnikov
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2202-6-55

Epidermal growth factor (EGF) withdrawal masks gene expression differences in the study of pituitary adenylate cyclase-activating polypeptide (PACAP) activation of primary neural stem cell proliferation
Cited by: 7
Author(s): Maria Sievertzon, Valtteri Wirta, Alex Mercer, Jonas Frisén, Joakim Lundeberg
Software Mentions: 2
Published: almost 21 years ago

10.1186/1471-2164-10-596

Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis
Cited by: 13
Author(s): Duccio Cavalieri, Enrica Calura, Chiara Romualdi, Emmanuela Marchi, Marijana Radonjić, Ben van Ommen, Michael Müller
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2164-11-467

A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database
Cited by: 15
Author(s): Kshitish K. Acharya, Darshan S. Chandrashekar, Neelima Chitturi, Hardik Shah, Varun Malhotra, Sreelakshmi Ks, H Deepti, Akhilesh Kumar Bajpai, Sravanthi Davuluri, Pranami Bora, L. Vaikunta Rao
Software Mentions: 2
Published: over 16 years ago

10.3390/molecules23071763

Genome Identification of B-BOX Gene Family Members in Seven Rosacea Species and Their Expression Analysis in Response to Flower Induction in Malus domestica
Cited by: 31
Author(s): Abdullah Shalmani, Shiliang Fan, Peng Jia, Guofang Li, Izhar Muhammad, Youmei Li, Rahat Sharif, Feng Dong, Xia Zuo, Ké Li, Kun-Ming Chen, Mingyu Han
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.molmet.2019.03.012

Dietary calories and lipids synergistically shape adipose tissue cellularity during postnatal growth
Cited by: 14
Author(s): Irina Meln, Gretchen Wolff, Thomas Gajek, Johanna Koddebusch, Sarah Lerch, Liza Harbrecht, Wujun Hong, Irem Bayindir‐Buchhalter, Damir Krunic, Hellmut G. Augustin, Alexandros Vegiopoulos
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0237463

Bio-activating ultrafine grain titanium: RNA sequencing reveals enhanced mechano-activation of osteoconduction on nanostructured substrates
Cited by: 4
Author(s): Rebecca A. Reiss, Terry C. Lowe, Johnny A. Sena, Oleg Makhnin, Melanie C. Connick, Patrick Erik Illescas, Casey F. Davis
Software Mentions: 2
Published: over 5 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

10.1186/1471-2164-7-49

Development of a chicken 5 K microarray targeted towards immune function
Cited by: 31
Author(s): Jacqueline Smith, David Speed, Paul Hocking, Richard Talbot, W.G.J. Degen, Virgil E.J.C. Schijns, Elizabeth J. Glass, David W. Burt
Software Mentions: 2
Published: over 20 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

10.1111/j.1365-2958.2009.06883.x

Role of the heat shock transcription factor, Hsf1, in a major fungal pathogen that is obligately associated with warm-blooded animals
Cited by: 89
Author(s): Susan M. Nicholls, Michelle Leach, Claire L. Priest, Alistair J. P. Brown
Software Mentions: 2
Published: over 16 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

10.1371/journal.pone.0200004

Activation of Nrf2 in the liver is associated with stress resistance mediated by suppression of the growth hormone-regulated STAT5b transcription factor
Cited by: 36
Author(s): John P. Rooney, Keiyu Oshida, Naresh Vasani, Beena Vallanat, Natalia Ryan, Brian N. Chorley, Xuting Wang, Douglas A. Bell, Kai Wu, Lauren M. Aleksunes, Curtis D. Klaassen, Thomas W. Kensler, J. Christopher Corton
Software Mentions: 2
Published: almost 8 years ago

10.1002/1878-0261.12068

Gain-of-function p53 activates multiple signaling pathways to induce oncogenicity in lung cancer cells
Cited by: 13
Author(s): Catherine Vaughan, S. K. Singh, Steven R. Grossman, Brad E. Windle, Sumitra Deb, Sumitra Deb
Software Mentions: 2
Published: about 9 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

10.1002/1878-0261.12107

Prognostic and functional role of subtype-specific tumor-stroma interaction in breast cancer
Cited by: 5
Author(s): Giuseppe Merlino, Patrizia Miodini, Maurizio Callari, Francesca D'Aiuto, Vera Cappelletti, Maria Grazia Daidone
Software Mentions: 2
Published: almost 9 years ago

10.1128/mBio.00966-18

cAMP Receptor Protein Controls Vibrio cholerae Gene Expression in Response to Host Colonization
Cited by: 41
Author(s): Jainaba Manneh-Roussel, James R. J. Haycocks, Andrés Magán, Nicolás Pérez-Soto, Kerstin Voelz, Andrew Camilli, Anne Marie Krachler, David C. Grainger
Software Mentions: 2
Published: almost 8 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

10.15252/msb.20145172

Cell cycle population effects in perturbation studies
Cited by: 103
Author(s): Eoghan O’Duibhir, Philip Lijnzaad, Joris J. Benschop, Tineke L. Lenstra, Dik van Leenen, Marian J. A. Groot Koerkamp, Thanasis Margaritis, Mariël Brok, Patrick Kemmeren, Frank C. P. Holstege
Software Mentions: 2
Published: about 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

10.7554/eLife.65722

Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast
Cited by: 18
Author(s): Rong Yu, Egor Vorontsov, Carina Sihlbom, Jens Nielsen
Software Mentions: 2
Published: over 5 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

10.1371/journal.pone.0248233

R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting
Cited by: 3
Author(s): Takeshi Kawakami, Meghan K. Jensen, Andrea Slavney, Petra E. Deane, Ausra Milano, Vandana Raghavan, Brett Ford, Erin T. Chu, Aaron J. Sams, Adam R. Boyko
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1004684

Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability
Cited by: 65
Author(s): Ayesha Hasan, Cristina Cotobal, Caia D. S. Duncan, Juan Mata
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0255679

Development of the petaloid bracts of a paleoherb species, Saururus chinensis
Cited by: 1
Author(s): Yanyan Zhao, Xuemei Zhang, Li D
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2229-11-113

Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thalianaseeds
Cited by: 48
Author(s): Peter C. McKeown, Sylvia Laouiellé-Duprat, Pjotr Prins, Philip Wolff, Marc W. Schmid, Mark T.A. Donoghue, Antoine Fort, Dorota Duszynska, Aurélie Comte, Nga T. Lao, Trevor Wennblom, G. Smant, Claudia Köhler, Ueli Grossniklaus, Charles Spillane
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0148957

Low Concordance between Gene Expression Signatures in ER Positive HER2 Negative Breast Carcinoma Could Impair Their Clinical Application
Cited by: 9
Author(s): Enora Laas, Peter Mallon, François P. Duhoux, Amina Hamidouche, Roman Rouzier, Fabien Reyal
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0235551

An iron-dependent metabolic vulnerability underlies VPS34-dependence in RKO cancer cells
Cited by: 7
Author(s): M.J. Kobylarz, Jonathan M. Goodwin, Kang Zhao, John W. Annand, Sarah Hevi, Ellen O’Mahony, Gregory McAllister, John S. Reece‐Hoyes, Qiong Wang, John Alford, Carsten Russ, Alicia Lindeman, Martin Beibel, Guglielmo Roma, Walter Carbone, Judith Knehr, Joseph Loureiro, Christophe Antczak, Dmitri Wiederschain, Leon O. Murphy, Suchithra Menon, Beat Nyfeler
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-213X-11-2

Targets downstream of Cdk8 in Dictyostelium development
Cited by: 4
Author(s): David Greene, Gareth Bloomfield, Jason Skelton, Alasdair Ivens, Catherine J. Pears
Software Mentions: 2
Published: over 15 years ago

10.3390/v4101844

miRNA Profiles of Monocyte-Lineage Cells Are Consistent with Complicated Roles in HIV-1 Restriction
Cited by: 31
Author(s): Jeanne M. Sisk, Janice E. Clements, Kenneth W. Witwer
Software Mentions: 2
Published: over 13 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

10.12688/wellcomeopenres.13119.2

Using mitoribosomal profiling to investigate human mitochondrial translation
Cited by: 2
Author(s): Fei Gao, Maria Wesołowska, Reuven Agami, Koos Rooijers, Fabricio Loayza‐Puch, Conor Lawless, RN Lightowlers, Z. Chrzanowska-Lightowlers
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2121-10-87

Global transcriptional response after exposure of fission yeast cells to ultraviolet light
Cited by: 6
Author(s): Henriette C. Skjølberg, Øyvind Fensgård, Hilde Nilsen, Beáta Grallert, Erik Boye
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0224854

Acute Influenza A virus outbreak in an enzootic infected sow herd: Impact on viral dynamics, genetic and antigenic variability and effect of maternally derived antibodies and vaccination
Cited by: 20
Author(s): Pia Ryt-Hansen, Anders Gorm Pedersen, Inge Larsen, Jesper Schak Krog, Charlotte Sonne Kristensen, Lars Erik Larsen
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2229-13-153

Transcriptome analysis of heat stress response in switchgrass (Panicum virgatumL.)
Cited by: 82
Author(s): Yongfang Li, Yixing Wang, Yuhong Tang, Vijaya Gopal Kakani, Ramamurthy Mahalingam
Software Mentions: 2
Published: over 12 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

10.1371/journal.pone.0036351

Transcriptome Sequencing Revealed Significant Alteration of Cortical Promoter Usage and Splicing in Schizophrenia
Cited by: 96
Author(s): Jing Qin Wu, Xi Wang, Natalie J. Beveridge, Paul A. Tooney, Rodney J. Scott, Vaughan J. Carr, Murray J. Cairns
Software Mentions: 2
Published: about 14 years ago

10.1186/s12885-021-08308-3

Identification of significant genes as prognostic markers and potential tumor suppressors in lung adenocarcinoma via bioinformatical analysis
Cited by: 15
Author(s): Mingze Lu, Xiao-Wen Fan, Wei-Lin Liao, Yijiao Li, Li Ma, Man Yuan, Rui Gu, Zhengdao Wei, Chao Wang, Hua Zhang
Software Mentions: 2
Published: about 5 years ago

10.1186/s13071-016-1945-z

Immune and biochemical responses in skin differ between bovine hosts genetically susceptible and resistant to the cattle tick Rhipicephalus microplus
Cited by: 32
Author(s): Alessandra Mara Franzin, Sandra Regina Maruyama, Gustavo García, Rosane Oliveira, José M. C. Ribeiro, Richard P. Bishop, Antônio Augusto Mendes Maia, Daniela D. Moré, Beatriz Rossetti Ferreira, Isabel Kinney Ferreira de Miranda Santos
Software Mentions: 2
Published: over 9 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

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962