bioconductor: ArrayExpress | Projects

10.1371/journal.pone.0110288

Integrated Analysis of Microarray Data of Atherosclerotic Plaques: Modulation of the Ubiquitin-Proteasome System
Cited by: 11
Author(s): Zhe Wang, Dong Guo, Bin Yang, Jian Wang, Rong Wang, Xiaowei Wang, Qunye Zhang
Software Mentions: 1
Published: over 11 years ago

10.1007/s10495-019-01542-y

17-Aminogeldanamycin selectively diminishes IRE1α-XBP1s pathway activity and cooperatively induces apoptosis with MEK1/2 and BRAFV600E inhibitors in melanoma cells of different genetic subtypes
Cited by: 12
Author(s): Aleksandra Mielczarek-Lewandowska, Małgorzata Sztiller-Sikorska, Marta Osrodek, Małgorzata Czyż, Mariusz L. Hartman
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0031867

Human Cryptochrome-1 Confers Light Independent Biological Activity in Transgenic Drosophila Correlated with Flavin Radical Stability
Cited by: 26
Author(s): Jacqueline Vieira, Alex R. Jones, Antoine Danon, Michiyo Sakuma, Nathalie Hoang, David Robles, Shirley Tait, Derren J. Heyes, Marie Christine Picot, Taishi Yoshii, Charlotte Helfrich‐Förster, Guillaume Soubigou, Jean Yves Coppée, André Klarsfeld, François Rouyer, Nigel S. Scrutton, Margaret Ahmad
Software Mentions: 1
Published: about 14 years ago

10.3390/ani10101924

Ovarian Transcriptomic Analysis Reveals Differential Expression Genes Associated with Cell Death Process after Selection for Ovulation Rate in Rabbits
Cited by: 0
Author(s): Marta Serna-García, Rosa Peiró, Eva Serna, M. A. Santacreu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0014207

Transcriptional Analysis Implicates Endoplasmic Reticulum Stress in Bovine Spongiform Encephalopathy
Cited by: 24
Author(s): Yue Tang, Wei Xiang, Linda A. Terry, Hans A. Kretzschmar, Otto Windl
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-10-119

Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes
Cited by: 58
Author(s): José Osorio y Fortéa, Emilie de La Llave, Béatrice Regnault, Jean‐Yves Coppée, Geneviève Milon, Thierry Lang, Éric Prina
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-6-174

Bacterial genome adaptation to niches: Divergence of the potential virulence genes in three Burkholderia species of different survival strategies
Cited by: 137
Author(s): Heenam Stanley Kim, Mark A. Schell, Yan Yu, Ricky L. Ulrich, Saul Sarria, William C. Nierman, David DeShazer
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pone.0088089

Phenotypic Modulation of Primary Vascular Smooth Muscle Cells by Short-Term Culture on Micropatterned Substrate
Cited by: 66
Author(s): Sea‐Jin Chang, Sang Yun Song, Jungsul Lee, Jonghee Yoon, Junseong Park, Sungyoung Choi, Je‐Kyun Park, Kyunghee Choi, Chulhee Choi
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0018088

Identification of a Gene Regulatory Network Necessary for the Initiation of Oligodendrocyte Differentiation
Cited by: 90
Author(s): Victoria A. Swiss, Tung Nguyen, Jason C. Dugas, Adiljan Ibrahim, Ben A. Barres, Ioannis P. Androulakis, Patrizia Casaccia
Software Mentions: 1
Published: about 15 years ago

10.1038/sdata.2015.77

Comprehensive systems biology analysis of a 7-month cigarette smoke inhalation study in C57BL/6 mice
Cited by: 25
Author(s): Sam Ansari, Karine Baumer, Stéphanie Boué, Sophie Dijon, Rémi Dulize, Kim Ekroos, Ashraf Elamin, Foong Clement, Emmanuel Guedj, Julia Hoeng, Nikolai V. Ivanov, Krishnan Subash, Patrice Leroy, Florian Martin, Céline Merg, Michael J. Peck, Manuel C. Peitsch, Blaine Phillips, Walter K. Schlage, Thomas Schneider, Marja Talikka, Bjoern Titz, Patrick Vanscheeuwijck, Emilija Veljkovic, Terhi Vihervaara, Grégory Vuillaume, Ching Qing Woon
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0153562

Competence Classification of Cumulus and Granulosa Cell Transcriptome in Embryos Matched by Morphology and Female Age
Cited by: 26
Author(s): Rehannah Borup, Lea Langhoff Thuesen, Claus Yding Andersen, Anders Nyboe-Andersen, Sören Ziebe, Ole Winther, Marie Louise Grøndahl
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-14-799

Chronic parasitization by Nosema microsporidia causes global expression changes in core nutritional, metabolic and behavioral pathways in honey bee workers (Apis mellifera)
Cited by: 85
Author(s): Holly L. Holt, Katherine A. Aronstein, Christina M. Grozinger
Software Mentions: 1
Published: over 13 years ago

10.1038/sdata.2017.125

Precision annotation of digital samples in NCBI’s gene expression omnibus
Cited by: 34
Author(s): Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D. Azad, Mohamad Omar Hadied, S. Mahmood Raza, Benjamin Abhishek Rayikanti, Bin Chen, Harikrishna Paik, Dvir Aran, Jordan Spatz, Daniel S. Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A. Musen, Atul J. Butte
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0056681

SGLT5 Reabsorbs Fructose in the Kidney but Its Deficiency Paradoxically Exacerbates Hepatic Steatosis Induced by Fructose
Cited by: 30
Author(s): Taku Fukuzawa, Motoharu Fukazawa, Otoya Ueda, Hideaki Shimada, Kito Aki, Mami Kakefuda, Yoshiaki Kawase, Naoko Wada, Chisato Goto, Naoshi Fukushima, Kou-ichi Jishage, Kazuo Honda, George L. King, Yojiro Kawabe
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2105-12-137

Assessing affymetrix GeneChip microarray quality
Cited by: 70
Author(s): Matthew N. McCall, Peter Murakami, Margus Lukk, Wolfgang Huber, Rafael A. Irizarry
Software Mentions: 1
Published: almost 15 years ago

10.1155/2018/1270483

Kynurenic Acid Protects against Thioacetamide-Induced Liver Injury in Rats
Cited by: 24
Author(s): Sebastian Marciniak, Artur Wnorowski, Katarzyna Smolińska, Beata Walczyna, Waldemar A. Turski, Tomasz Kocki, Piotr Paluszkiewicz, Jolanta Parada-Turska
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0074923

FHOD1, a Formin Upregulated in Epithelial-Mesenchymal Transition, Participates in Cancer Cell Migration and Invasion
Cited by: 49
Author(s): Maria Gardberg, Katja Kaipio, Laura Lehtinen, Piia Mikkonen, Vanina D. Heuser, Kati Talvinen, Kristiina Iljin, Caroline Kampf, Mathias Uhlén, Reidar Grénman, Mari Koivisto, Olli Carpén
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0070862

A Transcription Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumoniae
Cited by: 17
Author(s): Layla K. Mahdi, Esmaeil Ebrahimie, David L. Adelson, James C. Paton, Abiodun D. Ogunniyi
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-9-628

Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality
Cited by: 13
Author(s): Adam Ertel, Aydın Tözeren
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0046744

Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Brachypodium distachyon
Cited by: 89
Author(s): Lihong Chen, Wei Hu, Shenglong Tan, Min Wang, Zhanbing Ma, Shiyi Zhou, Xianwen Deng, Yang Zhang, Chao Huang, Guangxiao Yang, Guoqing He
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0038351

A Novel Strategy for Selection and Validation of Reference Genes in Dynamic Multidimensional Experimental Design in Yeast
Cited by: 49
Author(s): Ayca Cankorur-Cetinkaya, Elif Dereli, Serpil Eraslan, Muhammed Erkan Karabekmez, Duygu Dikicioglu, Betül Kırdar
Software Mentions: 1
Published: almost 14 years ago

10.1038/sdata.2018.29

Uniform resolution of compact identifiers for biomedical data
Cited by: 49
Author(s): Sarala M. Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A. McMurry, Niall Beard, Rafael C. Jiménez, Jeffrey S. Grethe, Henning Hermjakob, Maryann E. Martone, Tim W. Clark
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-13-323

Flexible and efficient genome tiling design with penalized uniqueness score
Cited by: 3
Author(s): Yang Du, Eduard Muráni, Siriluck Ponsuksili, Klaus Wimmers
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0021907

NRF2 Activation Restores Disease Related Metabolic Deficiencies in Olfactory Neurosphere-Derived Cells from Patients with Sporadic Parkinson's Disease
Cited by: 82
Author(s): Anthony Cook, Alejandra Vitale, Sugandha Ravishankar, Nicholas Matigian, Greg T. Sutherland, Jianguo Shan, Ratneswary Sutharsan, Christopher Perry, Peter A. Silburn, George D. Mellick, Murray L. Whitelaw, Christine A. Wells, Alan Mackay‐Sim, Stephen A. Wood
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0077263

Non-Specific dsRNA-Mediated Antiviral Response in the Honey Bee
Cited by: 113
Author(s): Michelle L. Flenniken, Raul Andino
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-11-714

Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources
Cited by: 22
Author(s): Camille Rustenholz, Pete E. Hedley, Jenny Morris, Frédéric Choulet, Catherine Feuillet, Robbie Waugh, Etienne Paux
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0018902

Deciphering the Role of RND Efflux Transporters in Burkholderia cenocepacia
Cited by: 67
Author(s): Silvia Bazzini, Claudia Udine, Andrea Saß, Maria Rosalia Pasca, Francesca Longo, Giovanni Emiliani, Marco Fondi, Elena Perrin, Francesca Decorosi, Carlo Viti, Luciana Giovannetti, Livia Leoni, Renato Fani, Giovanna Riccardi, Eshwar Mahenthiralingam, Silvia Buroni
Software Mentions: 1
Published: almost 15 years ago

10.1038/s41598-018-37591-7

Author Correction: Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 1
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Connor Rogerson, Christopher W. Bleaney, 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: 1
Published: about 7 years ago

10.1371/journal.pone.0142688

Comprehensive Survey of miRNA-mRNA Interactions Reveals That Ccr7 and Cd247 (CD3 zeta) are Posttranscriptionally Controlled in Pancreas Infiltrating T Lymphocytes of Non-Obese Diabetic (NOD) Mice
Cited by: 23
Author(s): Thaís A. Fornari, Paula B. Donate, Amanda Freire Assis, Cristiana Santos de Macedo, Elza T. Sakamoto-Hojo, Eduardo Antônio Donadi, Geraldo A. S. Passos
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-12-452

Histological and global gene expression analysis of the 'lactating' pigeon crop
Cited by: 43
Author(s): Meagan J Gillespie, Volker Häring, Kenneth A. McColl, Paul Monaghan, John A. Donald, Kevin R. Nicholas, Robert J. Moore, Tamsyn M. Crowley
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0116404

Protein Interactome of Muscle Invasive Bladder Cancer
Cited by: 12
Author(s): Akshay Bhat, Andreas Heinzel, Bernd Mayer, Paul Perco, Irmgard Mühlberger, Holger Husi, Axel S. Merseburger, Jérôme Zoidakis, Antonia Vlahou, Joost P. Schanstra, Harald Mischak, Vera Jankowski
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-10-S1-S54

Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data
Cited by: 3
Author(s): Dongxiao Zhu
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0099822

Underpinning Sustainable Vector Control through Informed Insecticide Resistance Management
Cited by: 50
Author(s): Edward Thomsen, Clare Strode, Kay Hemmings, Angela Hughes, Emmanuel Chanda, Mulenga Musapa, Mulakwa Kamuliwo, Faustina N. Phiri, Lucy Muzia, Javan Chanda, Alister Kandyata, Brian Chirwa, Kathleen Poer, Janet Hemingway, Charles S. Wondji, Hilary Ranson, Michael Coleman
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0103618

Gene Expression Analysis Suggests Bone Development-Related Genes GDF5 and DIO2 Are Involved in the Development of Kashin-Beck Disease in Children Rather than Adults
Cited by: 10
Author(s): Yan Wen, Na Zhang, Chunyan Li, Shulan He, Wenfeng Tan, Yanxia Lei, Zhang Qiang, Yu Sun, Jingjing Zheng, Xiong Guo
Software Mentions: 1
Published: over 11 years ago

10.1038/sdata.2019.21

The variable quality of metadata about biological samples used in biomedical experiments
Cited by: 48
Author(s): Rafael S. Gonçalves, Mark A. Musen
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2105-8-52

PASSIM – an open source software system for managing information in biomedical studies
Cited by: 23
Author(s): Juris Vīksna, Edgars Celms, Mārtiņš Opmanis, Kārlis Podnieks, Pēteris Ručevskis, Andris Zarins, Amy Barrett, Sudeshna Guha Neogi, Maria Krestyaninova, Mark I. McCarthy, Alvis Brāzma, Ugis Sarkans
Software Mentions: 1
Published: about 19 years ago

10.1186/1471-2164-13-407

Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins
Cited by: 75
Author(s): David Peris, Christian A. Lopes, Carmela Belloch, Amparo Querol, Eladio Barrio
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0063210

Characterization and Comparison of 2 Distinct Epidemic Community-Associated Methicillin-Resistant Staphylococcus aureus Clones of ST59 Lineage
Cited by: 49
Author(s): Chih‐Jung Chen, Clemens Unger, W. H. Hoffmann, Jodi A. Lindsay, Yhu-Chering Huang, Friedrich Götz
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-15-649

Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation
Cited by: 28
Author(s): Alison F. Richard, Paul Lyons, James E. Peters, Daniele Biasci, Shaun Flint, James C. Lee, Eoín McKinney, Richard M. Siegel, Kenneth G. C. Smith
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0148936

Expression of cagA, virB/D Complex and/or vacA Genes in Helicobacter pylori Strains Originating from Patients with Gastric Diseases
Cited by: 7
Author(s): Andrzej Szkaradkiewicz, Tomasz M. Karpiński, Krzysztof Linke, Przemysław Majewski, Dorota I. Rożkiewicz, Olga Goślińska-Kuźniarek
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0086643

Transcriptomic Meta-Analysis of Multiple Sclerosis and Its Experimental Models
Cited by: 27
Author(s): Barbara B. Raddatz, Florian Hansmann, Ingo Spitzbarth, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-11-142

TobEA: an atlas of tobacco gene expression from seed to senescence
Cited by: 61
Author(s): Kieron D. Edwards, Aureliano Bombarely, Geraint W. Story, F H Allen, Lukas A. Mueller, Steve Coates, Louise Jones
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-9-S6-S18

ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses
Cited by: 29
Author(s): Todd H. Stokes, J.T. Torrance, Henry Li, May D. Wang
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-11-343

Regulation of the cardiomyocyte transcriptome vs translatome by endothelin-1 and insulin: translational regulation of 5' terminal oligopyrimidine tract (TOP) mRNAs by insulin
Cited by: 15
Author(s): Thomais Markou, Andrew Keith Marshall, Timothy E. Cullingford, El Li Tham, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-11-709

Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans
Cited by: 62
Author(s): Jessica Cleiss-Arnold, Sandrine Koechler, Caroline Proux, Marie‐Laure Fardeau, Marie‐Agnès Dillies, Jean‐Yves Coppée, Florence Arsène-Ploetze, Philippe Bertin
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-8-70

Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation
Cited by: 338
Author(s): Birgit Kulterer, Gerald Friedl, Anita Jandrositz, Fátima Sánchez‐Cabo, Andreas Prokesch, Christine Paar, Marcel Scheideler, Reinhard Windhager, Karl‐Heinz Preisegger, Zlatko Trajanoski
Software Mentions: 1
Published: about 19 years ago

10.1186/1471-2164-9-375

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability
Cited by: 76
Author(s): Martin H. van Vliet, Fabien Reyal, Hugo M. Horlings, Marc J. van de Vijver, Marcel J. T. Reinders, Lodewyk Wessels
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-10-324

Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues
Cited by: 28
Author(s): Anita Grigoriadis, Gavin R. Oliver, Austin Tanney, Howard Kendrick, Matthew J. Smalley, Parmjit Jat, A. Munro Neville
Software Mentions: 1
Published: over 17 years ago

10.1038/s41597-019-0152-0

HENA, heterogeneous network-based data set for Alzheimer’s disease
Cited by: 33
Author(s): Elena Sügis, Jérôme Dauvillier, Anna Leontjeva, Priit Adler, Valérie Hindié, Thomas Moncion, Vincent Collura, Rachel Daudin, Yann Loe-Mie, Yann Hérault, Jean‐Charles Lambert, Henning Hermjakob, Tal Pupko, Jean-Christophe Rain, Ioannis Xénarios, Jaak Vilo, Michel Simonneau, Hedi Peterson
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0012667

Claudin 13, a Member of the Claudin Family Regulated in Mouse Stress Induced Erythropoiesis
Cited by: 16
Author(s): Pamela Thompson, Hannah Tipney, Andy Brass, Harry Noyes, Stephen J. Kemp, Jan Naessens, May Tassabehji
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-9-121

Transcriptome analysis of grain development in hexaploid wheat
Cited by: 183
Author(s): Yongfang Wan, Rebecca L Poole, Alison K. Huttly, C. Toscano-Underwood, Kevin A. Feeney, S. J. Welham, M. J. Gooding, Clare Mills, Keith J. Edwards, Peter R. Shewry, R. A. C. Mitchell
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0148308

Disruption of STAT5b-Regulated Sexual Dimorphism of the Liver Transcriptome by Diverse Factors Is a Common Event
Cited by: 41
Author(s): Keiyu Oshida, Naresh Vasani, David J. Waxman, J. Christopher Corton
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2164-7-266

Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray™
Cited by: 14
Author(s): Carole L. Yauk, Andrew Williams, Sherri E. Boucher, Lynn Berndt, Gu Zhou, Jiangxia Zheng, Andrea Rowan-Carroll, Hongyan Dong, Iain B. Lambert, George R. Douglas, Craig L.J. Parfett
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2105-10-441

The Medicago truncatula gene expression atlas web server
Cited by: 172
Author(s): Ji He, Vagner A. Benedito, Mingyi Wang, J. D. Murray, Patrick Xuechun Zhao, Yuhong Tang, Michael K. Udvardi
Software Mentions: 1
Published: over 16 years ago

10.1186/s12864-015-1342-6

The recent escalation in strength of pyrethroid resistance in Anopheles coluzzi in West Africa is linked to increased expression of multiple gene families
Cited by: 80
Author(s): Hyacinthe K. Toé, N’Falé Sagnon, Roch K. Dabiré, Hilary Ranson, Christopher M. Jones
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2105-11-610

BiologicalNetworks 2.0 - an integrative view of genome biology data
Cited by: 21
Author(s): Sergey Kozhenkov, Yulia Dubinina, Mayya Sedova, Amarnath Gupta, Julia Ponomarenko, Michael Baitaluk
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-14-376

Time-dependent changes in gene expression induced by secreted amyloid precursor protein-alpha in the rat hippocampus
Cited by: 35
Author(s): Margaret M. Ryan, Gary P. Morris, Bruce G. Mockett, Katie Bourne, Wickliffe C. Abraham, Warren P. Tate, Joanna M. Williams
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-14-336

A simple and reproducible breast cancer prognostic test
Cited by: 47
Author(s): Luigi Marchionni, Bahman Afsari, Donald Geman, Jeffrey T. Leek
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-16-S1-S11

Transcriptomics profiling study of breast cancer from Kingdom of Saudi Arabia revealed altered expression of Adiponectin and Fatty Acid Binding Protein4: Is lipid metabolism associated with breast cancer?
Cited by: 25
Author(s): Adnan Merdad, Sajjad Karim, Hans-Juergen Schulten, Jayapal Manikandan, Ashraf Dallol, Abdelbaset Buhmeida, Fatima Al-Thubaity, Mamdooh A GariI, Adeel Chaudhary, Adel M. Abuzenadah, Mohammed Al‐Qahtani
Software Mentions: 1
Published: about 11 years ago

10.3390/cancers12092450

Sustained Inflammatory Signalling through Stat1/Stat2/IRF9 Is Associated with Amoeboid Phenotype of Melanoma Cells
Cited by: 3
Author(s): Aneta Gandalovičová, Anna-Marie Šůchová, Vladimı́r Čermák, Ladislav Merta, Daniel Rösel, Jan Brábek
Software Mentions: 1
Published: over 5 years ago

10.3390/cancers12071790

Induction of Lysosome Membrane Permeabilization as a Therapeutic Strategy to Target Pancreatic Cancer Stem Cells
Cited by: 7
Author(s): Timothy P. Cash, Sonia Alcalá, María del Rosario Rico-Ferreira, Elena Hernández-Encinas, Jennifer García, María I. Albarrán, Sandra Valle, Javier Muñoz, Sonia Martínez-González, Carmen Blanco‐Aparicio, Joaquı́n Pastor, Manuel Serrano, Bruno Sáinz
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-42750-5

Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation
Cited by: 5
Author(s): Michael Laimighofer, Ramona Lickert, R. Fuerst, Fabian J. Theis, Christiane Winkler, Ezio Bonifacio, Anette‐Gabriele Ziegler, Jan Krumsiek
Software Mentions: 1
Published: almost 7 years ago

10.3390/cancers12020469

Personalized Assessment of Normal Tissue Radiosensitivity via Transcriptome Response to Photon, Proton and Carbon Irradiation in Patient-Derived Human Intestinal Organoids
Cited by: 8
Author(s): Ali Nowrouzi, Mathieu Sertorio, Mahdi Akbarpour, Maximilian Knoll, Damir Krunic, Matthew Kuhar, Christian Schwager, Stephan Brons, Jürgen Debus, Susanne I. Wells, James M. Wells, Amir Abdollahi
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2105-10-226

Information management for high content live cell imaging
Cited by: 4
Author(s): Daniel Jameson, David A. Turner, John Ankers, Stephnie Kennedy, Sheila Ryan, Neil Swainston, Tony Griffiths, David G. Spiller, Stephen G. Oliver, Mike White, Douglas B. Kell, Norman W. Paton
Software Mentions: 1
Published: over 16 years ago

10.3390/cancers12051133

Multi-Gene Prognostic Signatures and Prediction of Pathological Complete Response to Neoadjuvant Chemotherapy in ER-Positive, HER2-Negative Breast Cancer Patients
Cited by: 13
Author(s): Claudia Mazo, Stephen Barron, Catherine Mooney, William M. Gallagher
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13195-014-0070-5

PLD3 is accumulated on neuritic plaques in Alzheimer’s disease brains
Cited by: 35
Author(s): Jun‐ichi Satoh, Yoshihiro Kino, Yoji Yamamoto, Natsuki Kawana, Tsuyoshi Ishida, Yuko Saito, Kunimasa Arima
Software Mentions: 1
Published: over 11 years ago

10.3390/cancers12102738

Schlafen 12 Is Prognostically Favorable and Reduces C-Myc and Proliferation in Lung Adenocarcinoma but Not in Lung Squamous Cell Carcinoma
Cited by: 8
Author(s): Sarmad Al-Marsoummi, Jonathan Pacella, Kaylee Dockter, Matthew Soderberg, Sandeep K. Singhal, Emilie E. Vomhof-DeKrey, Marc D. Basson
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-10-151

MIMAS 3.0 is a Multiomics Information Management and Annotation System
Cited by: 16
Author(s): Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, Michael Primig
Software Mentions: 1
Published: almost 17 years ago

10.1186/2051-5960-2-23

The prognostic role of intragenic copy number breakpoints and identification of novel fusion genes in paediatric high grade glioma
Cited by: 20
Author(s): Diana Carvalho, Alan Mackay, Lynn Bjerke, Richard G. Grundy, Célia Lopes, Rui Manuel Reis, Chris Jones
Software Mentions: 1
Published: about 12 years ago

10.1186/s12864-016-2537-1

On the genome base composition of teleosts: the effect of environment and lifestyle
Cited by: 14
Author(s): Andrea Tarallo, Claudia Angelini, Remo Sanges, Mitsuharu Yagi, Claudio Agnisola, Giuseppe D’Onofrio
Software Mentions: 1
Published: about 10 years ago

10.1016/j.cell.2013.07.007

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
Cited by: 148
Author(s): Klara Stefflova, David Thybert, Michael D. Wilson, Ian Streeter, J. Aleksić, Panagiota Karagianni, Alvis Brāzma, David J. Adams, Iannis Talianidis, John C. Marioni, Paul Flicek, Duncan T. Odom
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-15-315

Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach
Cited by: 66
Author(s): Tommy Bengtsson, Deborah Weighill, Estelle Proux‐Wéra, Fredrik Levander, Svante Resjö, Dharani Dhar Burra, Laith Ibrahim Moushib, Pete E. Hedley, Erland Liljeroth, Dan Jacobson, Erik Alexandersson, Erik Andréasson
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-8-208

Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits
Cited by: 22
Author(s): Carl-Johan Rubin, Johan Lindberg, Carolyn Fitzsimmons, Peter Savolainen, Per Jensen, Joakim Lundeberg, Leif C. Andersson, Andreas Kindmark
Software Mentions: 1
Published: almost 19 years ago

10.1038/cddis.2017.109

Convergence and divergence between the transcriptional responses to Zika virus infection and prenatal irradiation
Cited by: 5
Author(s): Roel Quintens
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-016-2814-z

A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease
Cited by: 20
Author(s): Helgi B. Schiöth, Adrian Boström, Susan K. Murphy, Wiebke Erhart, Jochen Hampe, Cynthia A. Moylan, Jessica Mwinyi
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41419-019-1496-2

Enhancing folic acid metabolism suppresses defects associated with loss of Drosophila mitofusin
Cited by: 11
Author(s): Juan Garrido-Maraver, Ivana Celardo, Ana Carolina Oliveira Costa, Susann Lehmann, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 1
Published: about 7 years ago

10.1038/s41419-018-0681-z

CD24 regulates sorafenib resistance via activating autophagy in hepatocellular carcinoma
Cited by: 83
Author(s): Shan Lü, Yao Yao, Guolong Xu, Chao Zhou, Yuan Zhang, Jie Sun, Runqiu Jiang, Qing Shao, Yun Chen
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41419-020-2449-5

Enhanced fatty acid oxidation provides glioblastoma cells metabolic plasticity to accommodate to its dynamic nutrient microenvironment
Cited by: 59
Author(s): Shri Kant, Pravin Kesarwani, Antony Prabhu, Stewart F. Graham, Katie L. Buelow, Ichiro Nakano, Prakash Chinnaiyan
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41419-018-0933-y

The bHLH transcription factor DEC1 promotes thyroid cancer aggressiveness by the interplay with NOTCH1
Cited by: 25
Author(s): Cristina Gallo, Valentina Fragliasso, Benedetta Donati, Federica Torricelli, Annalisa Tameni, Simonetta Piana, Alessia Ciarrocchi
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-8-210

Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state
Cited by: 1
Author(s): Daniel Y L Yap, David K. Smith, Xue W Zhang, Jeffrey Hill
Software Mentions: 1
Published: over 19 years ago

10.1038/s41419-020-03129-x

Suppression of poised oncogenes by ZMYND8 promotes chemo-sensitization
Cited by: 10
Author(s): Shravanti Mukherjee, Santanu Adhikary, Shrikanth S. Gadad, Payel Mondal, Sabyasachi Sen, Ramesh Choudhari, Vipin Kumar Singh, Swagata Adhikari, Pratiti Mandal, Soumi Chaudhuri, Aditi Sengupta, Rajkumar Lakshmanaswamy, Partha Chakrabarti, Siddhartha Roy, Chandrima Das
Software Mentions: 1
Published: over 5 years ago

10.1111/j.1462-5822.2007.01099.x

During infection of epithelial cells Salmonella enterica serovar Typhimurium undergoes a time-dependent transcriptional adaptation that results in simultaneous expression of three type 3 secretion systems
Cited by: 230
Author(s): Isabelle Hautefort, Arthur R. Thompson, Sofia Eriksson-Ygberg, Mary L. Parker, Sacha Lucchini, Vittoria Danino, Roy J. Bongaerts, Norazah Ahmad, Mikael Rhen, Jay C. D. Hinton
Software Mentions: 1
Published: about 18 years ago

10.1111/cpr.13015

TSP50 promotes hepatocyte proliferation and tumour formation by activating glucose‐6‐phosphate dehydrogenase (G6PD)
Cited by: 12
Author(s): Xiaojun Zhang, Feng Gao, Huihan Ai, Shuyue Wang, Zhenbo Song, Lihua Zheng, Guannan Wang, Yu Sun, Yongli Bao
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2164-7-78

Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: Implications on genome evolution and plasticity
Cited by: 34
Author(s): Vattipally B Sreenu, Pankaj Kumar, Javaregowda Nagaraju, Hampapathalu A. Nagarajaram
Software Mentions: 1
Published: about 20 years ago

10.1016/j.celrep.2016.03.007

G9a/GLP Complex Maintains Imprinted DNA Methylation in Embryonic Stem Cells
Cited by: 90
Author(s): Tuo Zhang, Ausma Termanis, Burak Özkan, Xun X. Bao, Jayne Culley, Flávia de Lima Alves, Juri Rappsilber, Bernard Ramsahoye, Irina Stancheva
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2164-10-560

ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles
Cited by: 1
Author(s): Weizhong Li, Andrew Y. Gracey, Luciane V. Mello, Andy Brass, Andrew R. Cossins
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-10-153

Learning from microarray interlaboratory studies: measures of precision for gene expression
Cited by: 9
Author(s): David L. Duewer, Wendell Jones, Laura Reid, Marc Salit
Software Mentions: 1
Published: over 17 years ago

10.1016/j.crmeth.2021.100054

Retrospective cell lineage reconstruction in humans by using short tandem repeats
Cited by: 7
Author(s): Liming Tao, Ofir Raz, Zipora Marx, Manjusha Ghosh, Sandra Huber, Julia Greindl-Junghans, Tamir Biezuner, Shiran Amir, Lilach Milo, R Adar, Ronald Levy, Amos Onn, Noa Chapal-Ilani, Veronika Berman, Asaf Ben Arie, Guy Rom, Barak Oron, Ruth Halaban, Zbigniew T. Czyż, Melanie Werner-Klein, Christoph Klein, Ehud Shapiro
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2164-10-306

Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model
Cited by: 30
Author(s): Jin Hwan, Rui Yamaguchi, Satoru Miyano
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-8-401

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome
Cited by: 12
Author(s): Santiago P. Aubourg, Marie‐Laure Martin‐Magniette, Véronique Brunaud, Ludivine Taconnat, Frédérique Bitton, Sandrine Balzergue, Pauline E. Jullien, Mathieu Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny, Jean-Pierre Renou
Software Mentions: 1
Published: over 19 years ago

10.1038/srep15518

Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p
Cited by: 46
Author(s): Christopher J. Kershaw, Joseph L. Costello, David Talavera, William Rowe, Lydia M. Castelli, Paul F. G. Sims, Chris M. Grant, Mark P. Ashe, Simon J. Hubbard, Graham D. Pavitt
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-10-42

Positive correlation between gene coexpression and positional clustering in the zebrafish genome
Cited by: 28
Author(s): Yen Kaow Ng, Wei Wu, Louxin Zhang
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-12-620

An expression map for Anopheles gambiae
Cited by: 27
Author(s): Robert M. MacCallum, Seth Redmond, George K. Christophides
Software Mentions: 1
Published: over 14 years ago

10.3389/fcell.2021.673073

MeiosisOnline: A Manually Curated Database for Tracking and Predicting Genes Associated With Meiosis
Cited by: 4
Author(s): Xiaohua Jiang, Dingtao Zhao, Asim Ali, Bo Xu, Wei Liu, Jie Wen, Huan Zhang, Qinghua Shi, Yuanwei Zhang
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-9-340

Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis
Cited by: 87
Author(s): Marcel Scheideler, Christian Elabd, Laure‐Emmanuelle Zaragosi, Chiara Chiellini, Hubert Hackl, Fátima Sánchez‐Cabo, Sunaina Yadav, Kalina Duszka, Gerald Friedl, Christine Papak, Andreas Prokesch, Reinhard Windhager, Gérard Ailhaud, Christian Dani, Ez-Zoubir Amri, Zlatko Trajanoski
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-6-178

GPX-Macrophage Expression Atlas: A database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults
Cited by: 16
Author(s): Graeme R. Grimes, Stuart Moodie, John S. Beattie, Marie Craigon, Paul Dickinson, Thorsten Forster, Andrew D. Livingston, Muriel Mewissen, Kevin A. Robertson, Alan J. Ross, Garwin K. Sing, Peter Ghazal
Software Mentions: 1
Published: over 20 years ago

10.3389/fcell.2021.716501

GADD45B Is a Potential Diagnostic and Therapeutic Target Gene in Chemotherapy-Resistant Prostate Cancer
Cited by: 4
Author(s): Qiong Wang, Wanhua Wu, Zhe Gao, Kaiwen Li, Shirong Peng, Huiyang Fan, Zhongqiu Xie, Zhanfang Guo, Hai Huang
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-019-43795-2

Replication termination without a replication fork trap
Cited by: 20
Author(s): Elisa Galli, Jean-Luc Ferat, Jean-Michel Desfontaines, Marie-Eve Val, Ove Skovgaard, François‐Xavier Barre, Christophe Possoz
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-9-221

Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA
Cited by: 5
Author(s): Matthijs Raaben, Penn Whitley, Diane Bouwmeester, Robert A. Setterquist, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: almost 18 years ago

10.1038/s41598-019-46664-0

Virus Genotype-Dependent Transcriptional Alterations in Lipid Metabolism and Inflammation Pathways in the Hepatitis C Virus-infected Liver
Cited by: 18
Author(s): W. d’Avigdor, Magdalena A. Budzinska, M Lee, Roselind S. Lam, James G. Kench, Michael Stapelberg, Susan V. McLennan, Geoffrey C. Farrell, Jacob George, Geoffrey W. McCaughan, Thomas Tu, Nicholas Shackel
Software Mentions: 1
Published: over 6 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962