bioconductor: ArrayExpress | Projects

10.1371/journal.pone.0006880

Nuclear Receptor SHP Activates miR-206 Expression via a Cascade Dual Inhibitory Mechanism
Cited by: 44
Author(s): Guisheng Song, Lili Wang
Software Mentions: 1
Published: about 15 years ago

Distinct Genes Related to Drug Response Identified in ER Positive and ER Negative Breast Cancer Cell Lines
Cited by: 18
Author(s): Kui Shen, Shara D. Rice, David A. Gingrich, Dakun Wang, Mi Zhang, Chunqiao Tian, Zhenyu Ding, Stacey L. Brower, Paul R. Ervin, Michael J. Gabrin, George C. Tseng, Nan Song
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0028552

The Discovery of Putative Urine Markers for the Specific Detection of Prostate Tumor by Integrative Mining of Public Genomic Profiles
Cited by: 15
Author(s): Min Chen, Kai Wang, Liang Zhang, Cheng Li, Yongliang Yang
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2350-8-36

Cerebellar gene expression profiles of mouse models for Rett syndrome reveal novel MeCP2 targets
Cited by: 110
Author(s): ChaRandle Jordan, Hong Hua Li, Helen H. Kwan, Uta Francke
Software Mentions: 1
Published: over 17 years ago

10.1038/srep34719

Hepatic Deletion of Janus Kinase 2 Counteracts Oxidative Stress in Mice
Cited by: 23
Author(s): Madeleine Themanns, Kristina M. Mueller, Sonja M. Kessler, Nicole Golob-Schwarzl, Thomas Mohr, Doris Kaltenecker, Jérôme Bourgeais, Jamile Paier-Pourani, Katrin Friedbichler, Doris Schneller, Michaela Schlederer, Eva Zebedin-Brandl, Luigi Terracciano, Xiaonan Han, Lukas Kenner, Kay Uwe Wagner, Wolfgang Mikulits, Andrey V. Kozlov, Markus H. Heim, Fabrice Gouilleux, Johannes Haybaeck, Richard Moriggl
Software Mentions: 1
Published: about 8 years ago

10.1186/s12916-017-0929-y

A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes
Cited by: 40
Author(s): Jean‐Philippe Foy, Louis Bazire, Sandra Ortiz-Cuàran, Sophie Deneuve, Janice Kielbassa, Emilie Thomas, Alain Viari, Alain Puisieux, P. Goudot, Chloé Bertolus, Nicolas Foray, Youlia Kirova, Pierre Verrelle, Pierre Saintigny
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0018796

Stroma Regulates Increased Epithelial Lateral Cell Adhesion in 3D Culture: A Role for Actin/Cadherin Dynamics
Cited by: 31
Author(s): Karen Chambers, Joanna Pearson, Naveed Aziz, Peter O’Toole, David R. Garrod, Shona Lang
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0084187

High Expression of CD109 Antigen Regulates the Phenotype of Cancer Stem-Like Cells/Cancer-Initiating Cells in the Novel Epithelioid Sarcoma Cell Line ESX and Is Related to Poor Prognosis of Soft Tissue Sarcoma
Cited by: 53
Author(s): Makoto Emori, Tomohide Tsukahara, Masaki Murase, Masanobu Kano, Kenji Murata, Akiko Takahashi, Terufumi Kubo, Hiroko Asanuma, Kazuyo Yasuda, Vitaly Kochin, Mitsunori Kaya, Satoshi Nagoya, Jun Nishio, Hiroshi Iwasaki, Tomoko Sonoda, Tadashi Hasegawa, Toshihiko Torigoe, Takuro Wada, Toshihiko Yamashita, Noriyuki Sato
Software Mentions: 1
Published: almost 11 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: about 6 years ago

10.1186/s12916-016-0609-3

Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy
Cited by: 45
Author(s): Isobella Honeyborne, Timothy D. McHugh, Iitu Kuittinen, Anna Cichońska, Dimitrios Evangelopoulos, Katharina Ronacher, Paul D. van Helden, Stephen H. Gillespie, Delmiro Fernández-Reyes, Gerhard Walzl, Juho Rousu, Philip D. Butcher, Simon J. Waddell
Software Mentions: 1
Published: over 8 years ago

10.1186/s12879-016-1533-z

The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
Cited by: 13
Author(s): Steven T. Pullan, Jon C. Allnutt, Rebecca Devine, Kim A. Hatch, Rose E. Jeeves, Charlotte L. Hendon-Dunn, Philip Marsh, Joanna Bacon
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0010692

Skeletal Site-Related Variation in Human Trabecular Bone Transcriptome and Signaling
Cited by: 33
Author(s): Satya S. Varanasi, Ole Kristoffer Olstad, Daniel Swan, P. L. Sanderson, Vigdis T. Gautvik, Sjur Reppe, Roger M. Francis, Kaare M. Gautvik, Harish K. Datta
Software Mentions: 1
Published: over 14 years ago

10.1038/srep39262

Genome-wide Analysis of WD40 Protein Family in Human
Cited by: 37
Author(s): Xudong Zou, Xue-Jia Hu, Jing Ma, Tuan Li, Zhiqiang Ye, Yun Na Wu
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0100178

Chondroitin Sulfate Proteoglycan CSPG4 as a Novel Hypoxia-Sensitive Marker in Pancreatic Tumors
Cited by: 21
Author(s): Shereen Keleg, Titov Alexandr, Anette Heller, Thomas Giese, Christine Tjaden, Sufian S. Ahmad, Matthias M. Gaida, Andrea S. Bauer, Jens Werner, Nathalia A. Giese
Software Mentions: 1
Published: over 10 years ago

10.1186/s12865-017-0238-4

Cattle infection response network and its functional modules
Cited by: 5
Author(s): Hamid Beiki, A. Pakdel, A Nejati Javaremi, Ali Masoudi‐Nejad, James M. Reecy
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-13-49

Xanthomonas oryzae pv oryzae triggers immediate transcriptomic modulations in rice
Cited by: 29
Author(s): Rumdeep K Grewal, S. K. Gupta, Sampa Das
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0004344

The Staphylococcus aureus Response to Unsaturated Long Chain Free Fatty Acids: Survival Mechanisms and Virulence Implications
Cited by: 157
Author(s): John Kenny, Deborah Ward, Elisabet Josefsson, Ing-Marie Jonsson, Jason Hinds, Huw H. Rees, Jodi A. Lindsay, Andrej Tarkowski, Malcolm J. Horsburgh
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-10-330

BASE - 2nd generation software for microarray data management and analysis
Cited by: 50
Author(s): Johan Vallon‐Christersson, Nicklas Nordborg, Martin Svensson, Jari Häkkinen
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0089297

Meta-Analysis of Pathway Enrichment: Combining Independent and Dependent Omics Data Sets
Cited by: 43
Author(s): Alexander Kaever, Manuel Landesfeind, Kirstin Feussner, Burkhard Morgenstern, Ivo Feußner, Peter Meinicke
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-15-438

RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Cited by: 26
Author(s): Marta Vergara-Irigaray, María Fookes, Nicholas R. Thomson, Christoph M. Tang
Software Mentions: 1
Published: over 10 years ago

10.1038/srep45828

A 3q gene signature associated with triple negative breast cancer organ specific metastasis and response to neoadjuvant chemotherapy
Cited by: 19
Author(s): Jun Qian, Heidi Chen, Xiangming Ji, Rosana Eisenberg, A. Bapsi Chakravarthy, Ingrid A. Mayer, Pierre P. Massion
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0009426

The Genome of Streptococcus mitis B6 - What Is a Commensal?
Cited by: 105
Author(s): Dalia Denapaite, Reinhold Brückner, Michael Nuhn, Peter Reichmann, Bernhard Henrich, Patrick Maurer, Yvonne Schähle, Peter Selbmann, Wolfgang Zimmermann, R. Wambutt, Regine Hakenbeck
Software Mentions: 1
Published: over 14 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: almost 11 years ago

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: about 10 years ago

10.1038/s41598-017-01156-x

The centrosomal OFD1 protein interacts with the translation machinery and regulates the synthesis of specific targets
Cited by: 35
Author(s): Daniela Iaconis, Maria Monti, Mario Renda, Arianne van Koppen, Roberta Tammaro, Marco Chiaravalli, Flora Cozzolino, Paola Pignata, Claudia Crina, Piero Pucci, Alessandra Boletta, Vincenzo Belcastro, Rachel Giles, Enrico Maria Surace, Simone Gallo, Mario Pende, Brunella Franco
Software Mentions: 1
Published: over 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: over 12 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: about 10 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: almost 14 years ago

10.1186/s12864-016-2771-6

Transcriptomic response of yeast cells to ATX1 deletion under different copper levels
Cited by: 12
Author(s): Ayca Cankorur-Cetinkaya, Serpil Eraslan, Betül Kırdar
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-10-215

Dynamic changes in transcripts during regeneration of the secondary vascular system in Populus tomentosa Carr. revealed by cDNA microarrays
Cited by: 29
Author(s): Minjie Wang, Xiaoli Qi, Shutang Zhao, Shougong Zhang, Mengzhu Lu
Software Mentions: 1
Published: over 15 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: almost 11 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: over 13 years ago

10.1038/s41598-017-04709-2

DACH1 suppresses breast cancer as a negative regulator of CD44
Cited by: 29
Author(s): Hanxiao Xu, Shengnan Yu, Xun Yuan, Jing Xiong, Dong Kuang, Richard G. Pestell, Kongming Wu
Software Mentions: 1
Published: over 7 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: over 8 years ago

10.1186/1471-2164-11-682

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization
Cited by: 40
Author(s): Richard A. Lewis, Emma Laing, Nicholas E. E. Allenby, Giselda Bucca, Volker Brenner, Marcus Harrison, Andrzej M. Kierzek, Colin P. Smith
Software Mentions: 1
Published: almost 14 years ago

10.1038/s41598-017-05872-2

Functional and Transcriptomic Characterization of Peritoneal Immune-Modulation by Addition of Alanyl-Glutamine to Dialysis Fluid
Cited by: 12
Author(s): Rebecca Herzog, Lilian Kuster, Julia Powers Becker, Tobias Gluexam, Dietmar Pils, Andreas Spittler, Manoj Bhasin, Seth L. Alper, Andreas Vychytil, Christoph Aufricht, Klaus Kratochwill
Software Mentions: 1
Published: over 7 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: over 11 years ago

10.1038/s41598-017-06810-y

Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1
Cited by: 13
Author(s): James McCaffrey, Nicholas J.A. Webb, Toryn Poolman, Maryline Fresquet, Cressida Moxey, Leo Zeef, Ian J. Donaldson, David Ray, Rachel Lennon
Software Mentions: 1
Published: over 7 years ago

10.1186/1748-7188-4-5

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data
Cited by: 5
Author(s): Sahely Bhadra, Chiranjib Bhattacharyya, Nagasuma Chandra, I. Saira Mian
Software Mentions: 1
Published: over 15 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: about 11 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 11 years ago

10.1186/1471-2164-9-208

RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina
Cited by: 14
Author(s): Ravi Kiran Reddy Kalathur, Nicolas Gagnière, Guillaume Berthommier, Laetitia Poidevin, Wolfgang Raffelsberger, Raymond Ripp, Thierry Léveillard, Olivier Poch
Software Mentions: 1
Published: over 16 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: about 12 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: over 12 years ago

10.1186/1471-2105-11-433

Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization
Cited by: 10
Author(s): Ming Zhang, Yudong Zhang, Li Liu, Lijuan Yu, Shirley Tsang, Jian Tan, Wenhua Yao, Manjit S. Kang, Yong-Qiang An, Xing Fan
Software Mentions: 1
Published: over 14 years ago

10.18632/oncotarget.24644

MiR-21 over-expression and Programmed Cell Death 4 down-regulation features malignant pleural mesothelioma
Cited by: 12
Author(s): Lorenzo Nicolè, Rocco Cappellesso, Tiziana Sanavia, Vincenza Guzzardo, Ambrogio Fassina
Software Mentions: 1
Published: over 6 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: over 13 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: about 11 years ago

10.1186/1471-2164-10-575

Using transcriptome profiling to characterize QTL regions on chicken chromosome 5
Cited by: 13
Author(s): Guillaume Le Mignon, Colette Désert, Frédérique Pitel, Sophie Leroux, Olivier Demeure, Grégory Guernec, Behnam Abasht, Madeleine Douaire, Pascale Le Roy, Sandrine Lagarrigue
Software Mentions: 1
Published: almost 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: over 13 years ago

10.1038/s41598-017-12498-x

A dual targeted β-defensin and exome sequencing approach to identify, validate and functionally characterise genes associated with bull fertility
Cited by: 21
Author(s): Ronan Whiston, Emma K. Finlay, Matthew S. McCabe, Paul Cormican, Paul Flynn, A.R. Cromie, P. J. Hansen, A. Bruce Lyons, Seán Fair, Patrick Lonergan, Cliona O’ Farrelly, Kieran G. Meade
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: almost 9 years ago

10.1186/1471-2164-5-68

PEDRo: A database for storing, searching and disseminating experimental proteomics data
Cited by: 66
Author(s): Kevin Garwood, Thomas J. McLaughlin, Chris Garwood, Scott Joens, Norman Morrison, Christopher F Taylor, Kathleen M. Carroll, Caroline A. Evans, Anthony D. Whetton, Sarah R. Hart, David Stead, Zhikang Yin, Alistair J. P. Brown, Andrew Hesketh, Keith F. Chater, Lena Hansson, Muriel Mewissen, Peter Ghazal, Julie A. Howard, Kathryn S. Lilley, Simon J. Gaskell, Andy Brass, Simon J. Hubbard, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: about 20 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: almost 10 years ago

10.1186/1471-2105-8-447

Application of a correlation correction factor in a microarray cross-platform reproducibility study
Cited by: 7
Author(s): Kellie J. Archer, Catherine I. Dumur, G. Scott Taylor, Michael D. Chaplin, Anthony Guiseppi‐Elie, Geraldine M. Grant, Andrea Ferreira‐Gonzalez, Carleton T. Garrett
Software Mentions: 1
Published: about 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: over 10 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 10 years ago

10.1186/s12859-015-0854-z

Evaluation of O2PLS in Omics data integration
Cited by: 91
Author(s): Said el Bouhaddani, Jeanine J. Houwing-Duistermaat, Perttu Salo, Markus Perola, Geurt Jongbloed, Hae‐Won Uh
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2105-8-343

Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model
Cited by: 12
Author(s): Ryoko Morioka, Shigehiko Kanaya, Masami Yokota Hirai, Mitsuru Yano, Nagahisa Ogasawara, Kazuki Saito
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-16-S1-S2

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data
Cited by: 41
Author(s): Anna L Swan, Dov J. Stekel, Charlie Hodgman, David Allaway, Mohammed Hussein Al-Qahtani, Ali Mobasheri, Jaume Bacardit
Software Mentions: 1
Published: almost 10 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: about 11 years ago

10.1186/1471-2164-11-S1-S6

Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha
Cited by: 116
Author(s): Winston Koh, Chen Tian Sheng, Betty Tan, Qian Yi Lee, Vladimir A. Kuznetsov, Lim Sai Kiang, Vivek Tanavde
Software Mentions: 1
Published: almost 15 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: almost 9 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: almost 11 years ago

10.1186/1471-2164-9-291

Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium
Cited by: 66
Author(s): Alessio Sillo, Gareth Bloomfield, Alessandra Balest, Alessandra Balbo, Barbara Pergolizzi, Barbara Peracino, Jason Skelton, Alasdair Ivens, Salvatore Bozzaro
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2105-12-S10-S2

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses
Cited by: 14
Author(s): Mikhail G. Dozmorov, Jonathan D. Wren
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-11-478

Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes
Cited by: 11
Author(s): Michael Klutstein, Zahava Siegfried, Ariel Gispan, Shlomit Farkash-Amar, Guy Zinman, Ziv Bar‐Joseph, Giora Simchen, Itamar Simon
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-9-285

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
Cited by: 78
Author(s): Michael Boedigheimer, Russell D. Wolfinger, Michael Bass, Pierre R. Bushel, Jeff W. Chou, Matthew N. Cooper, J. Christopher Corton, Jennifer Fostel, Susan Hester, Janice S. Lee, Fenglong Liu, Jie Liu, Hui-Rong Qian, John Quackenbush, Syril Pettit, Karol L. Thompson
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-9-171

Transcriptional regulation by Poly(ADP-ribose) polymerase-1 during T cell activation
Cited by: 41
Author(s): Luis Sáenz, Juan José Lozano, Rut Valdor, Alberto Baroja‐Mazo, Pablo Ramı́rez, Pascual Parrilla, Pedro Aparicio, Lauro Sumoy, José Yélamos
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-10-350

Type I interferon receptor-independent and -dependent host transcriptional responses to mouse hepatitis coronavirus infection in vivo
Cited by: 17
Author(s): Matthijs Raaben, Marian J. A. Groot Koerkamp, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-15-S10-S4

Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation
Cited by: 2
Author(s): Alexis Vandenbon, Shunsuke Teraguchi, Osamu Takeuchi, Yutaka Suzuki, Daron M. Standley
Software Mentions: 1
Published: almost 10 years ago

10.18632/oncotarget.25736

A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing’s family of tumors
Cited by: 3
Author(s): Andrew J. Annalora, Shawn T. O’Neil, Jeremy D Bushman, James Summerton, Carol S. Marcus, Patrick L. Iversen
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: about 14 years ago

10.1186/1471-2164-12-113

Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns
Cited by: 21
Author(s): Daniel Báron, Emeric Dubois, Audrey Bihouée, Raluca Teusan, Marja Steenman, Philippe Jourdon, Armelle Magot, Yann Péreón, Reiner A. Veitia, Frédérique Savagner, Gérard Ramstein, Rémi Houlgatte
Software Mentions: 1
Published: almost 14 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: over 8 years ago

10.1186/1471-2164-8-22

Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population
Cited by: 73
Author(s): Chun Shi, Anna Użarowska, Milena Ouzunova, Matthias Landbeck, G. Wenzel, Thomas Lübberstedt
Software Mentions: 1
Published: almost 18 years ago

10.18632/oncotarget.26330

Whole genome duplication is an early event leading to aneuploidy in <i>IDH</i>-wild type glioblastoma
Cited by: 15
Author(s): Blandine Boisselier, Frédéric Dugay, Marc‐Antoine Belaud‐Rotureau, Anne Coutolleau, Emmanuel Garcion, Philippe Meneï, Philippe Guardiola, Audrey Rousseau
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-13-146

Meta-analysis of Chicken – Salmonella infection experiments
Cited by: 11
Author(s): M.F.W. te Pas, Ina Hulsegge, Dirkjan Schokker, M.A. Smits, Mark Fife, Rima Zoorob, Marie-Laure Endale, Johanna M.J. Rebel
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-018-21915-8

Morphine induces changes in the gut microbiome and metabolome in a morphine dependence model
Cited by: 144
Author(s): Fuyuan Wang, Jingjing Meng, Li Zhang, Timothy J. Johnson, Chi Chen, Sabita Roy
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-9-324

Topoisomerase II inhibition involves characteristic chromosomal expression patterns
Cited by: 7
Author(s): Susanne Reymann, Jürgen Borlak
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-15-333

MicroRNA profiling of rats with ochratoxin A nephrotoxicity
Cited by: 47
Author(s): Dai Qiu, Jingbo Zhao, Xiaozhe Qi, Wentao Xu, Xiaoyun He, Mingzhang Guo, Harsh Dweep, Wen‐Hsing Cheng, Yunbo Luo, Kai Xia, Norbert Gretz, Kunlun Huang
Software Mentions: 1
Published: over 10 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: over 15 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: about 4 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: over 4 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: over 13 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: almost 5 years ago

10.1038/s41598-018-24437-5

Deviations of the immune cell landscape between healthy liver and hepatocellular carcinoma
Cited by: 130
Author(s): Nataliya Rohr-Udilova, Florian Klinglmüller, Rolf Schulte‐Hermann, Judith Stift, Merima Herac, Martina Salzmann, Francesca Finotello, Gerald Timelthaler, Georg Oberhuber, Matthias Pinter, Thomas Reiberger, Erika Jensen‐Jarolim, Robert Eferl, Michael Trauner
Software Mentions: 1
Published: over 6 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: over 4 years ago

10.1038/s41598-018-24769-2

Profiling of 179 miRNA Expression in Blood Plasma of Lung Cancer Patients and Cancer-Free Individuals
Cited by: 32
Author(s): Ivan A. Zaporozhchenko, Evgeny S. Morozkin, Anastasia A. Ponomaryova, Elena Y. Rykova, Н. В. Чердынцева, А. А. Жеравин, O. A. Pashkovskaya, Evgeny Pokushalov, Valentin V. Vlassov, Pavel P. Laktionov
Software Mentions: 1
Published: over 6 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: about 4 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: almost 12 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: almost 16 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: almost 19 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 11 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: almost 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: almost 17 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: over 7 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: almost 14 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: over 5 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: over 6 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962