bioconductor: ArrayExpress | Projects

10.1371/journal.pone.0218950

Screening of urine identifies PLA2G16 as a field defect methylation biomarker for prostate cancer detection
Cited by: 6
Author(s): William E. Jarrard, Adam Schultz, Tyler Etheridge, Shivashankar Damodaran, Glenn O. Allen, David F. Jarrard, Bing Yang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0182455

Accounting for cell lineage and sex effects in the identification of cell-specific DNA methylation using a Bayesian model selection algorithm
Cited by: 6
Author(s): Nicole White, Miles C. Benton, Daniel W. Kennedy, Andrew Fox, Lyn R. Griffiths, Kerrie Mengersen
Software Mentions: 1
Published: over 8 years ago

10.1186/1472-6750-7-24

Comparison of target labeling methods for use with Affymetrix GeneChips
Cited by: 3
Author(s): William Lonergan, Toni Whistler, Suzanne D. Vernon
Software Mentions: 1
Published: almost 19 years ago

10.18632/oncotarget.16064

Integrated analysis of genes associated with poor prognosis of patients with colorectal cancer liver metastasis
Cited by: 30
Author(s): Zhenyuan Qian, Guobing Zhang, Guangyuan Song, Jing Shi, Lijie Gong, Yiping Mou, Yong Han
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0005349

The Genetic Requirements for Fast and Slow Growth in Mycobacteria
Cited by: 113
Author(s): Dany J. V. Beste, Mateu Espasa, Bhushan Bonde, Andrzej M. Kierzek, Graham R. Stewart, Johnjoe McFadden
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12915-019-0725-6

Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans
Cited by: 35
Author(s): Katharina Jovic, Jacopo Grilli, M.G. Sterken, L. Basten Snoek, J.A.G. Riksen, Stefano Allesina, J.E. Kammenga
Software Mentions: 1
Published: over 6 years ago

10.1093/bib/bbv013

Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures
Cited by: 9
Author(s): A. Modelska, Alessandro Quattrone, Angela Re
Software Mentions: 1
Published: about 11 years ago

10.1093/bib/bbv018

Adapting bioinformatics curricula for big data
Cited by: 38
Author(s): Anna C. Greene, Kristine A. Giffin, Casey S. Greene, Jason H. Moore
Software Mentions: 1
Published: about 11 years ago

10.1186/bcr2819

Prolactin-induced mouse mammary carcinomas model estrogen resistant luminal breast cancer
Cited by: 54
Author(s): Lisa M. Arendt, Debra E. Rugowski, Tara A Grafwallner-Huseth, Maria J. García-Barchino, Hallgeir Rui, Linda A. Schuler
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0053545

Transcript Profile Analyses of Maize Silks Reveal Effective Activation of Genes Involved in Microtubule-Based Movement, Ubiquitin-Dependent Protein Degradation, and Transport in the Pollination Process
Cited by: 15
Author(s): Xiao Hui Xu, Fang Wang, Hao Chen, Wei Sun, Xian Sheng Zhang
Software Mentions: 1
Published: over 13 years ago

10.18632/oncotarget.20284

Downregulation of microRNA-31 inhibits proliferation and induces apoptosis by targeting HIF1AN in human keloid
Cited by: 21
Author(s): Juan Zhang, Dan Xu, Na Li, Yan Li, Yongjing He, Xingbo Hu, Lechun Lyu, Li He
Software Mentions: 1
Published: over 8 years ago

10.1186/s13058-014-0441-7

Subtype-specific overexpression of the Rac-GEF P-REX1 in breast cancer is associated with promoter hypomethylation
Cited by: 32
Author(s): Laura Barrio-Real, Lorena Benedetti, Nora Engel, Yaping Tu, Soonweng Cho, Saraswati Sukumar, Marcelo G. Kazanietz
Software Mentions: 1
Published: over 11 years ago

10.18632/oncotarget.11215

Frequency of expression and generation of T-cell responses against antigens on multiple myeloma cells in patients included in the GMMG-MM5 trial
Cited by: 5
Author(s): Michael Schmitt, Angela Hückelhoven, Michael Hundemer, Anita Schmitt, Susanne Lipp, Martina Emde, Hans Salwender, Mathias Hänel, Katja Weisel, Uta Bertsch, Jan Dürig, Anthony D. Ho, Igor Wolfgang Blau, Hartmut Goldschmidt, Anja Seckinger, Dirk Hose
Software Mentions: 1
Published: over 9 years ago

10.1186/bcr3576

A mammosphere formation RNAi screen reveals that ATG4A promotes a breast cancer stem-like phenotype
Cited by: 106
Author(s): Jonas Michel Wolf, Dyah Laksmi Dewi, Johannes Fredebohm, Karin Müller‐Decker, Christa Flechtenmacher, Jörg D. Hoheisel, Michael Boettcher
Software Mentions: 1
Published: over 12 years ago

10.1186/bcr3048

Metastatic breast cancer cells inhibit osteoblast differentiation through the Runx2/CBFβ-dependent expression of the Wnt antagonist, sclerostin
Cited by: 89
Author(s): Daniel Mendoza-Villanueva, Leo Zeef, Paul Shore
Software Mentions: 1
Published: over 14 years ago

10.1186/bcr3191

Preclinical and clinical studies of estrogen deprivation support the PDGF/Abl pathway as a novel therapeutic target for overcoming endocrine resistance in breast cancer
Cited by: 39
Author(s): Marion T. Weigel, Zara Ghazoui, Anita K. Dunbier, Sunil Pancholi, Mitch Dowsett, Lesley-Ann Martin
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0093830

Staphylococcal Phenotypes Induced by Naturally Occurring and Synthetic Membrane-Interactive Polyphenolic β-Lactam Resistance Modifiers
Cited by: 24
Author(s): Lucía Palacios, Helena Rosado, Vicente Micol, Adriana E. Rosato, Patricia Bernal, Raquel Arroyo, Helen Grounds, James C. Anderson, Richard A. Stabler, Peter W. Taylor
Software Mentions: 1
Published: about 12 years ago

10.1186/s12915-018-0555-y

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0
Cited by: 37
Author(s): Alberto Santos-Zavaleta, Mishael Sánchez-Pérez, Heladia Salgado, David Alberto Velázquez-Ramírez, Socorro Gama-Castro, Víctor H. Tierrafría, Stephen J. W. Busby, Patricia Aquino, Xin Fang, Bernhard Ø. Palsson, James E. Galagan, Julio Collado‐Vides
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0048877

Clinical Value of Prognosis Gene Expression Signatures in Colorectal Cancer: A Systematic Review
Cited by: 79
Author(s): Rebeca Sanz‐Pamplona, Antoni Berenguer, David Cordero, Samantha Riccadonna, Xavier Solé, Marta Crous‐Bou, Elisabet Guinó, Xavier Sanjuán, Sebastiano Biondo, Antonio Soriano, Giuseppe Jurman, Gabriel Capellá, Cesare Furlanello, Vı́ctor Moreno
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0157484

Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression
Cited by: 36
Author(s): Aurora Torrente, Margus Lukk, Vincent Xue, Helen Parkinson, Johan Rung, Alvis Brāzma
Software Mentions: 1
Published: almost 10 years ago

10.1186/bcr3328

Low levels of Stat5a protein in breast cancer are associated with tumor progression and unfavorable clinical outcomes
Cited by: 64
Author(s): Amy R. Peck, Agnieszka K. Witkiewicz, Chengbao Liu, Alexander C. Klimowicz, Ginger A. Stringer, Edward Pequignot, Boris Freydin, Ning Yang, Adam Ertel, Thai H. Tran, Melanie A. Girondo, Anne Rosenberg, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, David L. Rimm, Anthony M. Magliocco, Terry Hyslop, Hallgeir Rui
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0138751

Interspecies Gene Name Extrapolation—A New Approach
Cited by: 5
Author(s): Roxana Cojocneanu, Cornelia Braicu, Cristian Bassi, Laura Pop, Ionelia Țăranu, Nicolae Dragoş, Dan L. Dumitrașcu, Massimo Negrini, Ioana Berindan‐Neagoe
Software Mentions: 1
Published: over 10 years ago

10.1186/s13058-017-0897-3

SPEN, a new player in primary cilia formation and cell migration in breast cancer
Cited by: 28
Author(s): Stéphanie Légaré, Catherine Chabot, Mark Basik
Software Mentions: 1
Published: over 8 years ago

10.1186/bcr3154

Functional characterization of the 19q12 amplicon in grade III breast cancers
Cited by: 61
Author(s): Rachael Natrajan, Alan Mackay, Paul M. Wilkerson, Maryou B. Lambros, Daniel Wetterskog, Mónica Arnedos, K-K. Shiu, Felipe C. Geyer, Anita Langerød, Bas Kreike, Fabien Reyal, Hugo M. Horlings, Marc J. van de Vijver, José Palacios, Britta Weigelt, Jorge S. Reis‐Filho
Software Mentions: 1
Published: about 14 years ago

10.1186/s40246-020-00269-1

Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals
Cited by: 4
Author(s): Andreanna Burman, Rolando García-Milián, Shannon Whirledge
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0000718

An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets
Cited by: 2,166
Author(s): Deborah R. Winter, Ben Vinegar, Hardeep Nahal, Ron Ammar, Greg Wilson, Nicholas J. Provart
Software Mentions: 1
Published: over 18 years ago

10.1038/s41416-018-0125-7

Transcriptomic immune profiling of ovarian cancers in paraneoplastic cerebellar degeneration associated with anti-Yo antibodies
Cited by: 12
Author(s): Clément Vialatte de Pémille, Giulia Berzero, Mathilde Small, Dimitri Psimaras, Marine Giry, Maïlys Daniau, Marc Sanson, Jean‐Yves Delattre, Jérôme Honnorat, Virginie Desestret, Agustí Alentorn
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0091334

Transcript Analysis Reveals a Specific HOX Signature Associated with Positional Identity of Human Endothelial Cells
Cited by: 52
Author(s): Mark Toshner, Benjamin J. Dunmore, Eoín McKinney, Mark Southwood, Paola Caruso, Paul D. Upton, John P Waters, Mark L. Ormiston, Jeremy N. Skepper, Gerard B. Nash, Radgonde Amer, Nicholas W. Morrell
Software Mentions: 1
Published: about 12 years ago

10.1186/s13068-019-1489-5

The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16
Cited by: 16
Author(s): Christian Arenas-López, Jessica Locker, Diego Orol, Frederik Walter, Tobias Busche, Jörn Kalinowski, Nigel P. Minton, Kármen Kovács, Klaus Winzer
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12915-014-0060-x

Developmental stage-dependent metabolic regulation during meiotic differentiation in budding yeast
Cited by: 9
Author(s): Thomas Walther, Fabien Létisse, Lindsay Peyriga, Ceren Alkım, Yuchen Liu, Aurélie Lardenois, Hélène Martin-Yken, Jean‐Charles Portais, Michael Primig, Jean François
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0039148

Leukemia Gene Atlas – A Public Platform for Integrative Exploration of Genome-Wide Molecular Data
Cited by: 48
Author(s): Katja Hebestreit, Sören Gröttrup, Daniel Emden, Jannis Veerkamp, Christian Rückert, Hans-Ulrich Klein, Carsten Müller‐Tidow, Martin Dugas
Software Mentions: 1
Published: almost 14 years ago

10.1186/s13068-019-1446-3

Combining loss of function of FOLYLPOLYGLUTAMATE SYNTHETASE1 and CAFFEOYL-COA 3-O-METHYLTRANSFERASE1 for lignin reduction and improved saccharification efficiency in Arabidopsis thaliana
Cited by: 17
Author(s): Hong-Li Xie, Nancy L. Engle, Sivasankari Venketachalam, Chang Geun Yoo, Jaime Barros, Mitch Lecoultre, Nikki Howard, Guifen Li, Liang Sun, Ashutosh Srivastava, Sivakumar Pattathil, Yunqiao Pu, Michael G. Hahn, Arthur J. Ragauskas, Richard S. Nelson, Richard A. Dixon, Timothy J. Tschaplinski, Elison B. Blancaflor, Yuhong Tang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0010027

ERK1/2 Signaling Dominates Over RhoA Signaling in Regulating Early Changes in RNA Expression Induced by Endothelin-1 in Neonatal Rat Cardiomyocytes
Cited by: 35
Author(s): Andrew Keith Marshall, Oliver Barrett, Timothy E. Cullingford, Achchuthan Shanmugasundram, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: about 16 years ago

10.3390/biomedicines9091251

Ladostigil Attenuates Induced Oxidative Stress in Human Neuroblast-like SH-SY5Y Cells
Cited by: 4
Author(s): Keren Zohar, Elyad Lezmi, Tsiona Eliyahu, Michal Linial
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0126837

A Ranking-Based Meta-Analysis Reveals Let-7 Family as a Meta-Signature for Grade Classification in Breast Cancer
Cited by: 14
Author(s): Yasemin Öztemur, Tufan Bekmez, Alp Aydos, Işık G. Yuluğ, Birkan Bozkurt, Bala Gür Dedeoğlu
Software Mentions: 1
Published: almost 11 years ago

10.1155/2021/6529255

Synthetic Evaluation of MicroRNA-1-3p Expression in Head and Neck Squamous Cell Carcinoma Based on Microarray Chips and MicroRNA Sequencing
Cited by: 1
Author(s): Yubing Chen, Mingjiang Liu, Jin Hu, Bo Peng, Luo Dai, Sifan Wang, H. Rosie Xing, Baoju Wang, Zhan He Wu
Software Mentions: 1
Published: over 4 years ago

10.18632/oncotarget.17926

Increased transcriptional and metabolic capacity for lipid metabolism in the peripheral zone of the prostate may underpin its increased susceptibility to cancer
Cited by: 11
Author(s): Omar Al Kadhi, Μαρία Τράκα, Antonietta Melchini, Perla Troncoso‐Rey, Wiktor Jurkowski, Marianne Defernez, Purnima Pachori, Robert Mills, Richard Y. Ball, Richard Mithen
Software Mentions: 1
Published: almost 9 years ago

10.1093/hmg/ddw417

Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus
Cited by: 25
Author(s): Christopher A. Odhams, Andrea Cortini, Lingyan Chen, Amy L. Roberts, Ana Viñuela, Alfonso Buil, Kerrin S. Small, Emmanouil T. Dermitzakis, David L. Morris, Timothy J. Vyse, Deborah S. Cunninghame Graham
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0134595

Distinct Responses of Mycobacterium smegmatis to Exposure to Low and High Levels of Hydrogen Peroxide
Cited by: 22
Author(s): Xiaojing Li, Wu Jun, Jiao Han, Yongfei Hu, Kaixia Mi
Software Mentions: 1
Published: over 10 years ago

10.1155/2017/9614596

Detecting the Candidate Gender Determinants by Bioinformatic Prediction of miRNAs and Their Targets from Transcriptome Sequences of the Male and Female Flowers in Salix suchowensis
Cited by: 1
Author(s): Suyun Wei, Ning Ye, Tongming Yin
Software Mentions: 1
Published: over 9 years ago

10.1155/2015/724715

Detecting Key Genes Regulated by miRNAs in Dysfunctional Crosstalk Pathway of Myasthenia Gravis
Cited by: 11
Author(s): Yuze Cao, Jianjian Wang, Huixue Zhang, Qinghua Tian, Lixia Chen, Shangwei Ning, Peifang Liu, Xiang Sun, Xiaoyu Lu, Chang Eun Song, Shuai Zhang, Bo Xiao, Lihua Wang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0023466

Transcriptome Analysis of Potato Leaves Expressing the Trehalose-6-Phosphate Synthase 1 Gene of Yeast
Cited by: 31
Author(s): Mihály Kondrák, Ferenc Marincs, Balázs Kalapos, Zsófia Juhász, Zsófia Bánfalvi
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0064011

Transcriptional Analysis of Temporal Gene Expression in Germinating Clostridium difficile 630 Endospores
Cited by: 61
Author(s): Marcin Dembek, Richard A. Stabler, Adam A. Witney, Brendan W. Wren, Neil F. Fairweather
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0016192

Global Transcriptional Analysis of Spontaneous Sakacin P-Resistant Mutant Strains of Listeria monocytogenes during Growth on Different Sugars
Cited by: 20
Author(s): Girum Tadesse Tessema, Trond Møretrø, Lars Snipen, Lars Axelsson, Kristine Naterstad
Software Mentions: 1
Published: over 15 years ago

10.1242/bio.047530

Forcing contacts between mitochondria and the endoplasmic reticulum extends lifespan in a Drosophila model of Alzheimer's disease
Cited by: 25
Author(s): Juan Garrido-Maraver, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-016-1106-6

Gene expression prediction using low-rank matrix completion
Cited by: 40
Author(s): Arnav Kapur, Kshitij Marwah, Gil Alterovitz
Software Mentions: 1
Published: almost 10 years ago

10.1093/bioinformatics/btz959

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences
Cited by: 41
Author(s): Rachel Drysdale, Charles E. Cook, Robert Petryszak, Vivienne Baillie-Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl, Jürgen Haas, Jerry Lanfear, Rodrigo López, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Elixir Core Data Resource Forum, Niklas Blomberg, Christine Durinx, Johanna McEntyre
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0003563

HFR1 Is Crucial for Transcriptome Regulation in the Cryptochrome 1-Mediated Early Response to Blue Light in Arabidopsis thaliana
Cited by: 20
Author(s): Xiaoning Zhang, Yingjie Wu, John W. Tobias, Brian P. Brunk, Gerald F. Deitzer, Dongmei Li
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0026905

Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis
Cited by: 25
Author(s): Qinghua Xu, Shujuan Ni, Fei Wu, Fang Liu, Xun Ye, Bruno Mougin, Meng Xia, Xiang Du
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-15-53

Eureka-DMA: an easy-to-operate graphical user interface for fast comprehensive investigation and analysis of DNA microarray data
Cited by: 1
Author(s): Sagi Abelson
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-8-400

CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes
Cited by: 45
Author(s): Gert Sclep, Joke Allemeersch, Robin Liechti, Björn De Meyer, Jim Beynon, Rishikesh P. Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, Martin Kuiper, Pierre Hilson
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0053341

Identification of Gene Clusters Associated with Host Adaptation and Antibiotic Resistance in Chinese Staphylococcus aureus Isolates by Microarray-Based Comparative Genomics
Cited by: 12
Author(s): Henan Li, Chunjiang Zhao, Hongbin Chen, Feifei Zhang, Wenqiang He, Xiaojuan Wang, Qi Wang, Ruifu Yang, Dongsheng Zhou, Hui Wang
Software Mentions: 1
Published: over 13 years ago

10.1093/bioinformatics/btw545

PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations
Cited by: 12
Author(s): Jamie Soul, Sara Dunn, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0215452

Array expression meta-analysis of cancer stem cell genes identifies upregulation of PODXL especially in DCC low expression meningiomas
Cited by: 4
Author(s): Hans-Juergen Schulten, Deema Hussein
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0039718

Transcriptional Profiling of Serogroup B Neisseria meningitidis Growing in Human Blood: An Approach to Vaccine Antigen Discovery
Cited by: 25
Author(s): Åsa K. Hedman, Mingshi Li, Paul R. Langford, J. Simon Kroll
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0065058

Retinoic Acid-Activated Ndrg1a Represses Wnt/β-catenin Signaling to Allow Xenopus Pancreas, Oesophagus, Stomach, and Duodenum Specification
Cited by: 20
Author(s): Tiejun Zhang, Xiaogang Guo, Yonglong Chen
Software Mentions: 1
Published: almost 13 years ago

10.1186/s13046-016-0403-2

Microarray-based identification of genes associated with cancer progression and prognosis in hepatocellular carcinoma
Cited by: 33
Author(s): Fuqiang Yin, Liuyang Shu, Xia Liu, Ting Li, Tao Peng, Yueli Nan, Shu Li, Xianmin Zeng, Xiaoqiang Qiu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0061262

The Expression of Glyceraldehyde-3-Phosphate Dehydrogenase Associated Cell Cycle (GACC) Genes Correlates with Cancer Stage and Poor Survival in Patients with Solid Tumors
Cited by: 41
Author(s): Dunrui Wang, Daniel R. Moothart, Douglas R. Lowy, Xiaolan Qian
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0006408

Transcriptomic Profiling of Central Nervous System Regions in Three Species of Honey Bee during Dance Communication Behavior
Cited by: 40
Author(s): Moushumi Sen Sarma, Sandra L. Rodriguez-Zas, Feng Hong, Sheng Zhong, Gene E. Robinson
Software Mentions: 1
Published: over 16 years ago

10.1186/s13046-016-0477-x

Nomogram integrating gene expression signatures with clinicopathological features to predict survival in operable NSCLC: a pooled analysis of 2164 patients
Cited by: 18
Author(s): Jianhui Wu, Lizhi Zhou, Lixia Huang, Jincui Gu, Shaoli Li, Baomo Liu, Jinlun Feng, Yunyun Zhou
Software Mentions: 1
Published: over 9 years ago

10.1093/bioinformatics/btt019

CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data
Cited by: 841
Author(s): Gabriela Bindea, Jérôme Galon, Bernhard Mlecnik
Software Mentions: 1
Published: about 13 years ago

10.1093/bioinformatics/btt108

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data
Cited by: 13
Author(s): George Y. Wu, Jason T. Yustein, Matthew N. McCall, Michael J. Zilliox, Rafael A. Irizarry, Karen Zeller, Chi V. Dang, Hongkai Ji
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0063184

Database Citation in Full Text Biomedical Articles
Cited by: 30
Author(s): Şenay Kafkas, Jee-Hyub Kim, Johanna McEntyre
Software Mentions: 1
Published: almost 13 years ago

10.1093/bioinformatics/btx739

SATORI: a system for ontology-guided visual exploration of biomedical data repositories
Cited by: 9
Author(s): Fritz Lekschas, Nils Gehlenborg
Software Mentions: 1
Published: over 8 years ago

10.1093/bioinformatics/btz731

Metric learning on expression data for gene function prediction
Cited by: 10
Author(s): Stavros Makrodimitris, Marcel J. T. Reinders, Roeland C. H. J. van Ham
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0016419

Genetic Variation in Spatio-Temporal Confined USA300 Community-Associated MRSA Isolates: A Shift from Clonal Dispersion to Genetic Evolution?
Cited by: 15
Author(s): Neeltje Carpaij, Rob J. L. Willems, Thomas W. Rice, Robert A. Weinstein, Jason Hinds, Adam A. Witney, Jodi A. Lindsay, Marc J. M. Bonten, Ad C. Fluit
Software Mentions: 1
Published: about 15 years ago

10.1186/s13046-017-0568-3

miR-500a-3p promotes cancer stem cells properties via STAT3 pathway in human hepatocellular carcinoma
Cited by: 60
Author(s): Chonghe Jiang, Jianting Long, Baoxian Liu, Ming Xu, Wei Wang, Xian-Jin Xie, Xiaolin Wang, Ming Kuang
Software Mentions: 1
Published: over 8 years ago

10.1186/1756-0381-7-18

ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions
Cited by: 20
Author(s): Philip Zimmermann, Stefan Bleuler, Oliver Laule, Florian Martin, Nikolai V. Ivanov, Prisca Campanoni, Karen K. Oishi, Nicolas Lugon-Moulin, Markus Wyss, Tomás Hrúz, Wilhelm Gruissem
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0184317

Differential expression of tetraspanin superfamily members in dendritic cell subsets
Cited by: 19
Author(s): Malou Zuidscherwoude, Kuntal Worah, Alie van der Schaaf, Sonja I. Buschow, Annemiek B. van Spriel
Software Mentions: 1
Published: over 8 years ago

10.1186/1756-0381-1-9

Fast approximate hierarchical clustering using similarity heuristics
Cited by: 18
Author(s): Meelis Kull, Jaak Vilo
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0021463

E-Cadherin Acts as a Regulator of Transcripts Associated with a Wide Range of Cellular Processes in Mouse Embryonic Stem Cells
Cited by: 29
Author(s): Francesca Soncin, Lisa Mohamet, Sarah Ritson, Kate Hawkins, Nicoletta Bobola, Leo Zeef, Catherine L.R. Merry, Christopher M. Ward
Software Mentions: 1
Published: almost 15 years ago

10.1186/s13046-017-0642-x

Drug repurposing for the treatment of glioblastoma multiforme
Cited by: 56
Author(s): Claudia Abbruzzese, Silvia Matteoni, Michele Signore, Luca Cardone, Kavindra Nath, Jerry D. Glickson, Marco G. Paggi
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0023944

A Stratified Transcriptomics Analysis of Polygenic Fat and Lean Mouse Adipose Tissues Identifies Novel Candidate Obesity Genes
Cited by: 45
Author(s): Nicholas M. Morton, Yvonne B. Nelson, Zoi Michailidou, Emma M. Di Rollo, Lynne Ramage, Patrick W. F. Hadoke, Jonathan R. Seckl, L. Bünger, Simon Horvat, Christopher J. Kenyon, Donald R. Dunbar
Software Mentions: 1
Published: over 14 years ago

10.1186/1756-0381-4-15

Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation
Cited by: 13
Author(s): Pablo Christian Echeverria, Fedor Forafonov, Deo Prakash Pandey, Guillaume Mühlebach, Didier Picard
Software Mentions: 1
Published: almost 15 years ago

10.1186/1746-6148-6-44

Feasibility of a liver transcriptomics approach to assess bovine treatment with the prohormone dehydroepiandrosterone (DHEA)
Cited by: 19
Author(s): Jeroen C.W. Rijk, Ad Peijnenburg, Peter J.M. Hendriksen, Johan M. Van Hende, M.J. Groot, Michel W. F. Nielen
Software Mentions: 1
Published: over 16 years ago

10.1186/s12894-015-0056-z

An online tool for evaluating diagnostic and prognostic gene expression biomarkers in bladder cancer
Cited by: 14
Author(s): Garrett M. Dancik
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0075290

Coordinated and Interactive Expression of Genes of Lipid Metabolism and Inflammation in Adipose Tissue and Liver during Metabolic Overload
Cited by: 22
Author(s): Wen Miin Liang, Giulia Tonini, Petra Mulder, Thomas Kelder, Marjan van Erk, Anita M. van den Hoek, Rob Mariman, Peter Y. Wielinga, Michela Baccini, Teake Kooistra, Annibale Biggeri, Robert Kleemann
Software Mentions: 1
Published: over 12 years ago

10.1186/1752-0509-2-58

Short time-series microarray analysis: Methods and challenges
Cited by: 43
Author(s): Xuewei Wang, Ming Tsang Wu, Lirong Zheng, Christina Chan
Software Mentions: 1
Published: almost 18 years ago

10.1186/s13046-019-1147-6

Anti-CD166/4-1BB chimeric antigen receptor T cell therapy for the treatment of osteosarcoma
Cited by: 42
Author(s): Yitian Wang, Wei Yu, Jian Zhu, Junjie Wang, Kaishun Xia, Chengzhen Liang, Huimin Tao
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0041683

Identification of Novel Markers of Mouse Fetal Ovary Development
Cited by: 43
Author(s): Huijun Chen, Jodie Palmer, Rathi D Thiagarajan, Marcel E. Dinger, Emmanuelle Lesieur, Hansheng Sheng Chiu, Alexandra Schulz, Cassy M. Spiller, Sean M. Grimmond, Melissa H. Little, Peter Koopman, Dagmar Wilhelm
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0138889

Adipose Tissue Dysfunction and Altered Systemic Amino Acid Metabolism Are Associated with Non-Alcoholic Fatty Liver Disease
Cited by: 63
Author(s): Sulin Cheng, Reija Autio, Ronald Borra, Xiaowei Ojanen, Leiting Xu, Timo Törmäkangas, Markku Alén
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0009894

Functional Clustering of Periodic Transcriptional Profiles through ARMA(p,q)
Cited by: 32
Author(s): Ning Li, Timothy L. McMurry, Arthur Berg, Zhong Wang, Scott A. Berceli, Rongling Wu
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0020938

COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia
Cited by: 24
Author(s): Kristof Engelen, Qiang Fu, Pieter Meysman, Aminael Sánchez-Rodríguez, Riet De Smet, Kim Lemmens, Ana Carolina Fierro, Kathleen Marchal
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0006759

Butyrate-Induced Transcriptional Changes in Human Colonic Mucosa
Cited by: 143
Author(s): Steven Vanhoutvin, Freddy J. Troost, Henrike M. Hamer, Patrick Lindsey, Ger H. Koek, Daisy Jonkers, Andrea Kodde, Koen Venema, Robert Jan Brummer
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0075882

microRNA-22 Promotes Heart Failure through Coordinate Suppression of PPAR/ERR-Nuclear Hormone Receptor Transcription
Cited by: 72
Author(s): Priyatansh Gurha, Tiannan Wang, Ashley H. Larimore, Yassine Sassi, Cei Abreu‐Goodger, Maricela Ramirez, Anilkumar K. Reddy, Stefan Engelhardt, George E. Taffet, Xander H.T. Wehrens, Mark L. Entman, Antony Rodríguez
Software Mentions: 1
Published: over 12 years ago

10.1186/1752-0509-4-164

ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work
Cited by: 69
Author(s): Gregor Warsow, Boris Greber, Steffi Falk, Clemens Harder, Marcin Siatkowski, Sandra Schordan, Anup Som, Nicole Endlich, Hans R. Schöler, Dirk Repsilber, Karlhans Endlich, Georg Fuellen
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2105-11-389

GeneBrowser 2: an application to explore and identify common biological traits in a set of genes
Cited by: 6
Author(s): Joel P. Arrais, João Fernandes, João E. Pereira, José Luís Oliveira
Software Mentions: 1
Published: over 15 years ago

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: over 16 years ago

10.1371/journal.pone.0040900

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: almost 14 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: over 14 years ago

10.1186/1752-0509-4-62

Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis
Cited by: 51
Author(s): Elizabeth Allen, Annick Moing, Timothy M. D. Ebbels, Mickaël Maucourt, A. D. Tomos, Dominique Rolin, Mark A. Hooks
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12859-015-0870-z

Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment
Cited by: 30
Author(s): Roman Hornung, Anne‐Laure Boulesteix, David Causeur
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-5-125

A Systems Biology Strategy for Predicting Similarities and Differences of Drug Effects: Evidence for Drug-specific Modulation of Inflammation in Atherosclerosis
Cited by: 15
Author(s): Robert Kleemann, Svetlana Bureeva, Ally Perlina, Jim Kaput, Lars Verschuren, Peter Y. Wielinga, Eva Hurt-Camejo, Yuri Nikolsky, Ben van Ommen, Teake Kooistra
Software Mentions: 1
Published: over 15 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: almost 15 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: over 12 years ago

10.1002/ijc.25688

Zinc deficiency activates S100A8 inflammation in the absence of COX‐2 and promotes murine oral‐esophageal tumor progression
Cited by: 37
Author(s): Shao Gui Wan, Cristian Taccioli, Yubao Jiang, Hongping Chen, Karl J. Smalley, Kun Huang, Xiu Ping Liu, John L. Farber, Carlo M. Croce, Louise Y.Y. Fong
Software Mentions: 1
Published: over 15 years ago

10.1186/1752-0509-4-86

Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems
Cited by: 7
Author(s): Michał Dąbrowski, Norbert Dojer, Małgorzata Zawadzka, Jakub Mieczkowski, Bożena Kamińska
Software Mentions: 1
Published: almost 16 years ago

10.1186/1752-0509-3-86

Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network
Cited by: 39
Author(s): Osnat Atias, Benny Chor, Daniel Chamovitz
Software Mentions: 1
Published: over 16 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: almost 16 years ago

10.1186/1471-2105-9-379

MiMiR – an integrated platform for microarray data sharing, mining and analysis
Cited by: 18
Author(s): Christopher Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L. Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Timothy J. Aitman, Laurence Gamé
Software Mentions: 1
Published: over 17 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962