bioconductor: ArrayExpress | Projects

10.1371/journal.pone.0127427

MiRNA Profiles in Lymphoblastoid Cell Lines of Finnish Prostate Cancer Families
Cited by: 9
Author(s): Daniel Fischer, Tiina Wahlfors, Henna Mattila, Hannu Oja, Teuvo L.J. Tammela, Johanna Schleutker
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0042853

Cationic Amphiphilic Drugs Are Potent Inhibitors of Yeast Sporulation
Cited by: 8
Author(s): Ulrich Schlecht, Robert P. St.Onge, Thomas Walther, Jean François, Ronald W. Davis
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0152859

R-Spondins Are Expressed by the Intestinal Stroma and are Differentially Regulated during Citrobacter rodentium- and DSS-Induced Colitis in Mice
Cited by: 19
Author(s): Ellen S. Kang, Mitra Yousefi, Samantha Gruenheid
Software Mentions: 1
Published: over 10 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: about 7 years ago

10.1371/journal.pone.0036301

Cystatin A, a Potential Common Link for Mutant Myocilin Causative Glaucoma
Cited by: 20
Author(s): Kit Kennedy, S. A. AnithaChristy, LaKisha K. Buie, Teresa Borrás
Software Mentions: 1
Published: over 14 years ago

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: about 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: almost 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: over 17 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: about 7 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

10.1371/journal.pgen.1000286

Field-Caught Permethrin-Resistant Anopheles gambiae Overexpress CYP6P3, a P450 That Metabolises Pyrethroids
Cited by: 293
Author(s): Pie Müller, Emma Warr, Bradley J. Stevenson, Pasquale Pignatelli, John C. Morgan, Andrew Steven, Alexander Egyir Yawson, Sara N. Mitchell, Hilary Ranson, Janet Hemingway, Mark J. I. Paine, Martin J. Donnelly
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0031577

Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells
Cited by: 34
Author(s): Jakub Orzechowski Westholm, Susanna Tronnersjö, Niklas Nordberg, Ida Olsson, Jan Komorowski, Hans Ronne
Software Mentions: 1
Published: over 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: over 12 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: almost 14 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: about 10 years ago

10.1038/s41598-019-49124-x

Gene Regulatory Networks in Peripheral Mononuclear Cells Reveals Critical Regulatory Modules and Regulators of Multiple Sclerosis
Cited by: 8
Author(s): Perumal Gnanakkumaar, Ram Murugesan, Shiek S. S. J. Ahmed
Software Mentions: 1
Published: almost 7 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: almost 11 years ago

10.1371/journal.pone.0052875

Transcriptional Profiling of Human Dendritic Cell Populations and Models - Unique Profiles of In Vitro Dendritic Cells and Implications on Functionality and Applicability
Cited by: 88
Author(s): Kristina Lundberg, Ann-Sofie Albrekt, Inge Nelissen, Saskia J. Santegoets, Tanja D. de Gruijl, S. Gibbs, Malin Lindstedt
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0005198

Host Iron Binding Proteins Acting as Niche Indicators for Neisseria meningitidis
Cited by: 32
Author(s): Philip W. Jordan, N. Saunders
Software Mentions: 1
Published: over 17 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: about 19 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: over 12 years ago

10.1371/journal.pone.0036776

MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer
Cited by: 9
Author(s): Akhilesh Kumar Bajpai, Sravanthi Davuluri, Darshan S. Chandrashekar, Ilakya Selvarajan, Mahalakshmi Dinakaran, Kshitish K. Acharya
Software Mentions: 1
Published: over 14 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: about 14 years ago

10.1371/journal.pgen.1000846

Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome
Cited by: 220
Author(s): Juan M. Vaquerizas, Ritsuko Suyama, Jop Kind, Kota Miura, Nicholas M. Luscombe, Asifa Akhtar
Software Mentions: 1
Published: over 16 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: over 16 years ago

10.1371/journal.pone.0131335

Alkbh8 Regulates Selenocysteine-Protein Expression to Protect against Reactive Oxygen Species Damage
Cited by: 64
Author(s): Lauren Endres, Ulrike Begley, Ryan R. Clark, Cheng Gu, Agnieszka Dziergowska, Andrzej Małkiewicz, J. Andrés Melendez, Peter C. Dedon, Thomas J. Begley
Software Mentions: 1
Published: about 11 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: over 11 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: about 11 years ago

10.1371/journal.pone.0013069

Hfq Is a Global Regulator That Controls the Pathogenicity of Staphylococcus aureus
Cited by: 58
Author(s): Yu Liu, Na Wu, Jing Dong, Yaping Gao, Xin Zhang, Chunhua Mu, Ningsheng Shao, Guangxiao Yang
Software Mentions: 1
Published: almost 16 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: almost 15 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: over 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

10.1371/journal.pone.0111168

The Porphyromonas gingivalis Ferric Uptake Regulator Orthologue Binds Hemin and Regulates Hemin-Responsive Biofilm Development
Cited by: 14
Author(s): Catherine A. Butler, Stuart G. Dashper, Lianyi Zhang, Christine A. Seers, Helen Mitchell, Deanne V. Catmull, Michelle D. Glew, Jacqueline E. Heath, Yan Tan, Hasnah Begum Said Ghulam Khan, Eric C. Reynolds
Software Mentions: 1
Published: almost 12 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: almost 18 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: almost 15 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

10.1371/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: over 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: about 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: about 13 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: over 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: about 17 years ago

10.1371/journal.pone.0150982

A Human "eFP" Browser for Generating Gene Expression Anatograms
Cited by: 10
Author(s): Rohan Patel, Erin T. Hamanishi, Nicholas J. Provart
Software Mentions: 1
Published: over 10 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: about 13 years ago

10.1371/journal.pgen.1007256

Broken replication forks trigger heritable DNA breaks in the terminus of a circular chromosome
Cited by: 35
Author(s): Anurag Kumar Sinha, Christophe Possoz, Adeline Durand, Jean-Michel Desfontaines, François‐Xavier Barre, David R. F. Leach, Bertrand Michel
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0064483

Identification of Novel Tissue-Specific Genes by Analysis of Microarray Databases: A Human and Mouse Model
Cited by: 36
Author(s): Yan Song, Jinsoo Ahn, Young Ho Suh, Michael Davis, Kichoon Lee
Software Mentions: 1
Published: about 13 years ago

10.3390/cells9010142

Dissecting Mechanisms of Melanoma Resistance to BRAF and MEK Inhibitors Revealed Genetic and Non-Genetic Patient- and Drug-Specific Alterations and Remarkable Phenotypic Plasticity
Cited by: 41
Author(s): Mariusz L. Hartman, Małgorzata Sztiller-Sikorska, Anna Gajos-Michniewicz, Małgorzata Czyż
Software Mentions: 1
Published: over 6 years ago

10.3390/cells8121554

Transcriptional Characterization of Stage I Epithelial Ovarian Cancer: A Multicentric Study
Cited by: 9
Author(s): Enrica Calura, Matteo Ciciani, Andrea Sambugaro, Lara Paracchini, Giuseppe Benvenuto, Salvatore Milite, Paolo Martini, Luca Beltrame, Flaminia Zane, Robert Fruscio, Martina Delle Marchette, Fulvio Borella, Germana Tognon, Antonella Ravaggi, Dionyssios Katsaros, Eliana Bignotti, Franco Odicino, Maurizio D’Incalci, Sergio Marchini, Chiara Romualdi
Software Mentions: 1
Published: over 6 years ago

10.3390/cells10030674

Acyl–Acyl Carrier Protein Desaturases and Plant Biotic Interactions
Cited by: 11
Author(s): Sami Kazaz, Romane Miray, Sébastien Baud
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0009748

Cardiac Deletion of Smyd2 Is Dispensable for Mouse Heart Development
Cited by: 68
Author(s): Florian Diehl, Mark A. Brown, Machteld J. van Amerongen, Tatyana Novoyatleva, Astrid Wietelmann, June V. Harriss, Fulvia Ferrazzi, Thomas Boettger, Richard P. Harvey, Philip W. Tucker, Felix B. Engel
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0017154

Human Primary Adipocytes Exhibit Immune Cell Function: Adipocytes Prime Inflammation Independent of Macrophages
Cited by: 170
Author(s): Kees Meijer, Marcel P. de Vries, Saad Al-Lahham, Marcel Bruinenberg, Desireé Weening, Martijn Dijkstra, Niels J. Kloosterhuis, Roelof Jan van der Leij, H van der Want, Bart-Jan Kroesen, Roel J. Vonk, Farhad Rezaee
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0026985

Transcriptomics Responses in Marine Diatom Thalassiosira pseudonana Exposed to the Polycyclic Aromatic Hydrocarbon Benzo[a]pyrene
Cited by: 51
Author(s): Ralph Carvalho, Stephanie K. Bopp, Teresa Lettieri
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0008408

Expression Profiling the Temperature-Dependent Amphibian Response to Infection by Batrachochytrium dendrobatidis
Cited by: 144
Author(s): Laia Ribas, Mingshi Li, Benjamin J. Doddington, Jacques Robert, Judith A. Seidel, J. Simon Kroll, Lyle B. Zimmerman, Nicholas C Grassly, Trenton W. J. Garner, Matthew C. Fisher
Software Mentions: 1
Published: over 16 years ago

10.1186/s13148-018-0542-8

Epigenetic regulation of ID4 in breast cancer: tumor suppressor or oncogene?
Cited by: 20
Author(s): Daniela Nasif, Emanuel Campoy, Sergio Laurito, Richard L. Branham, Guillermo Urrutia, María Roqué, Marı́a Teresita Branham
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0187920

Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization
Cited by: 15
Author(s): Thiago Jonas Nakayama, Fabiana Aparecida Rodrigues, N. Neumaier, Juliana Marcolino-Gomes, Hugo Bruno Correa Molinari, Thaís Ribeiro Santiago, Eduardo Fernandes Formighieri, Marcos Fernando Basso, J. R. B. Farias, Beatriz Marti Emygdio, A. Oliveira, Ângela Diniz Campos, Aluízio Borém, Frank G. Harmon, L. M. Mertz-Henning, Alexandre Lima Nepomuceno
Software Mentions: 1
Published: over 8 years ago

10.1186/s13148-020-00851-3

Genome-wide DNA methylation profiles of low- and high-grade adenoma reveals potential biomarkers for early detection of colorectal carcinoma
Cited by: 32
Author(s): Fan Jian, Jun Li, Shicheng Guo, Chengcheng Tao, Haikun Zhang, Wenjing Wang, Ying Zhang, Dake Zhang, Shigang Ding, Changqing Zeng
Software Mentions: 1
Published: over 6 years ago

10.1007/s10585-016-9810-1

Prognostic value of 5-microRNA based signature in T2-T3N0 colon cancer
Cited by: 49
Author(s): Maciej Bobowicz, Marcin Skrzypski, Piotr Czapiewski, Michał Marczyk, Agnieszka Maciejewska, Michał Jankowski, Anna Szulgo-Paczkowska, Wojciech Zegarski, Ryszard Pawłowski, Joanna Polańska, Wojciech Biernat, Janusz Jaśkiewicz, Jacek Jassem
Software Mentions: 1
Published: about 10 years ago

10.1093/cid/ciaa503

The Current Status of Enteric Fever Diagnostics and Implications for Disease Control
Cited by: 2
Author(s): Stephen Baker, Christoph J. Blohmke, Mailis Maes, Peter I Johnston, Thomas C. Darton
Software Mentions: 1
Published: about 6 years ago

10.1038/cti.2015.17

Expression profiling pre‐diabetic mice to uncover drugs with clinical application to type 1 diabetes
Cited by: 2
Author(s): Dimeng Pang, Katharine M. Irvine, Ahmed M. Mehdi, Helen E. Thomas, Mark Harris, Emma E. Hamilton‐Williams, Ranjeny Thomas
Software Mentions: 1
Published: about 11 years ago

10.1186/2001-1326-3-7

Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development
Cited by: 108
Author(s): Maria Frantzi, Akshay Bhat, Agnieszka Latosinska
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0040538

Temporal Profiling of Gene Networks Associated with the Late Phase of Long-Term Potentiation In Vivo
Cited by: 50
Author(s): Margaret M. Ryan, Brigid Ryan, Madeleine Kyrke-Smith, Barbara Logan, Warren P. Tate, Wickliffe C. Abraham, Joanna M. Williams
Software Mentions: 1
Published: about 14 years ago

10.1038/s42003-019-0281-1

SnRK2 protein kinases represent an ancient system in plants for adaptation to a terrestrial environment
Cited by: 69
Author(s): Akihisa Shinozawa, Ryoko Otake, Daisuke Takezawa, Taishi Umezawa, Kenji Kono, Keisuke Tanaka, Anna Amagai, Shin-nosuke Ishikawa, Yusuke Hara, Yasuko Kamisugi, Andrew C. Cuming, Koichi Hori, Hiroyuki Ohta, Fumiyuki Takahashi, Kazuo Shinozaki, Takahisa Hayashi, Teruaki Taji, Yoichi Sakata
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-69254-x

Identification of potential biomarkers for predicting the early onset of diabetic cardiomyopathy in a mouse model
Cited by: 8
Author(s): Rabia Johnson, Xolisa Nxele, Martin Cour, Nonhlakanipho F. Sangweni, Tracey Jooste, Nkanyiso Hadebe, Ebrahim Samodien, Mongi Benjeddou, Mikateko Mazino, Johan Louw, Sandrine Lecour
Software Mentions: 1
Published: about 6 years ago

10.1155/2021/8020067

Identification of Immune-Related Genes in Sepsis due to Community-Acquired Pneumonia
Cited by: 1
Author(s): Yanyan Li, Jiqin Wang, Yuzhen Li, Chunyan Liu, Xia Gong, Yijie Zhuang, Liang Chen, Kai Sun
Software Mentions: 1
Published: almost 5 years ago

10.1016/j.csbj.2017.10.001

Challenges in the Setup of Large-scale Next-Generation Sequencing Analysis Workflows
Cited by: 41
Author(s): Pranav Kulkarni, Peter Frommolt
Software Mentions: 1
Published: over 9 years ago

10.1016/j.csbj.2016.10.003

Determining the Molecular Pathways Underlying the Protective Effect of Non-Steroidal Anti-Inflammatory Drugs for Alzheimer's Disease: A Bioinformatics Approach
Cited by: 12
Author(s): Alejo J. Nevado‐Holgado, Simon Lovestone
Software Mentions: 1
Published: over 9 years ago

10.1016/j.csbj.2018.02.001

An Artificial Neural Network Integrated Pipeline for Biomarker Discovery Using Alzheimer's Disease as a Case Study
Cited by: 42
Author(s): Dimitrios Zafeiris, Sergio Rutella, Graham Ball
Software Mentions: 1
Published: over 8 years ago

10.1186/cc12893

Induced expression and functional effects of aquaporin-1 in human leukocytes in sepsis
Cited by: 31
Author(s): Alice G. Vassiliou, Nikolaos A. Maniatis, Stylianos E. Orfanos, Zafeiria Mastora, Edison Jahaj, Triantafyllos Paparountas, Apostolos Armaganidis, Charis Roussos, Vassilis Aidinis, Αναστασία Κοτανίδου
Software Mentions: 1
Published: over 13 years ago

10.2174/138920208786847935

Meta Analysis of Gene Expression Data within and Across Species
Cited by: 34
Author(s): Ana Carolina Fierro, Filip Vandenbussche, Kristof Engelen, Yves Van de Peer, Kathleen Marchal
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0152997

Overexpression and Biological Function of Ubiquitin-Specific Protease 42 in Gastric Cancer
Cited by: 19
Author(s): Kezuo Hou, Zhihua Zhu, Yong Wang, Chunhui Zhang, Shanshan Yu, Qingqing Zhu, Bo Yan
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0093175

Renal Tissue Thawed for 30 Minutes Is Still Suitable for Gene Expression Analysis
Cited by: 5
Author(s): Yi Ma, Xiaonan Kang, Weijun Ding, Haozheng Yang, Ye Wang, Jin Zeng, Yiran Huang, Hongyue Dai
Software Mentions: 1
Published: over 12 years ago

10.1016/j.dib.2016.11.049

Microarray dataset on the genome-wide expression profile of an M. smegmatis amtR mutant (JR258) compared to M. smegmatis mc 2 155
Cited by: 2
Author(s): Michael Petridis, Gregory M. Cook
Software Mentions: 1
Published: over 9 years ago

10.1016/j.dib.2018.11.135

Gene ontology analysis of transcriptome data from DMBA-induced mammary tumors of rats fed a high-corn oil and a high-extra virgin olive oil diet
Cited by: 1
Author(s): Raquel Escrich, Marta Cubedo, Eduard Escrich, Raquel Moral
Software Mentions: 1
Published: over 7 years ago

10.1093/database/bax101

CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system
Cited by: 21
Author(s): Yi-Fang Lee, Chien‐Yueh Lee, Liang‐Chuan Lai, Mong‐Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang
Software Mentions: 1
Published: over 8 years ago

10.1093/database/bax071

SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets
Cited by: 12
Author(s): Jin Li, Ching-San Tseng, Antonio Federico, Franjo Ivankovic, Yu-Shan Huang, Alfredo Ciccodicola, Maurice S. Swanson, Peng Yu
Software Mentions: 1
Published: over 9 years ago

10.1093/database/baz058

Chickspress: a resource for chicken gene expression
Cited by: 15
Author(s): Fiona M. McCarthy, Ken Pendarvis, Amanda M. Cooksey, Cathy Gresham, Matt Bomhoff, Sean Davey, Eric Lyons, Tad S. Sonstegard, Susan M. Bridges, Shane C. Burgess
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0053391

Characterization of the Humoral Immune Response during Staphylococcus aureus Bacteremia and Global Gene Expression by Staphylococcus aureus in Human Blood
Cited by: 69
Author(s): P. Martijn den Reijer, Nicole Lemmens-den Toom, Samantha Kant, Susan V. Snijders, Hélène Boelens, Mehri Tavakol, Nelianne J. Verkaik, Alex van Belkum, Henri A. Verbrugh, Willem J. B. van Wamel
Software Mentions: 1
Published: over 13 years ago

10.1093/database/bay116

YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast
Cited by: 1
Author(s): Wei Wu, Hao Ping Tu, Yu Chu, Torbjörn E. M. Nordling, Yan Yuan Tseng, Hungjiun Liaw
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1005153

A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression
Cited by: 43
Author(s): Marta Garrido, Benjamin Frage, Patrick R. Wright, Anke Becker
Software Mentions: 1
Published: over 11 years ago

10.1093/database/bax098

PCOSBase: a manually curated database of polycystic ovarian syndrome
Cited by: 9
Author(s): Nor Afiqah‐Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti‐Azura Mohamed‐Hussein
Software Mentions: 1
Published: over 9 years ago

10.1093/database/bay054

RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins
Cited by: 4
Author(s): Jin Li, Su-Ping Deng, Jacob Vieira, James Thomas, Valerio Costa, Ching-San Tseng, Franjo Ivankovic, Alfredo Ciccodicola, Peng Yu
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1002398

Widespread Cotranslational Formation of Protein Complexes
Cited by: 104
Author(s): Caia D. S. Duncan, Juan Mata
Software Mentions: 1
Published: over 14 years ago

10.1093/database/baz023

YESdb: integrative analysis of environmental stress in yeast
Cited by: 1
Author(s): Evi Berchtold, Gergely Csaba, Ralf Zimmer
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0134866

Transcriptomic Profiling of Virus-Host Cell Interactions following Chicken Anaemia Virus (CAV) Infection in an In Vivo Model
Cited by: 19
Author(s): Efstathios S. Giotis, Lisa Rothwell, Alistair Scott, Tuanjun Hu, Richard Talbot, D. Todd, David W. Burt, Elizabeth J. Glass, Pete Kaiser
Software Mentions: 1
Published: about 11 years ago

10.1186/1479-5876-9-72

SULFs in human neoplasia: implication as progression and prognosis factors
Cited by: 68
Author(s): Caroline Bret, Jérôme Moreaux, Jean‐François Schved, Dirk Hose, Bernard Klein
Software Mentions: 1
Published: about 15 years ago

10.1093/database/bay059

IsopiRBank: a research resource for tracking piRNA isoforms
Cited by: 14
Author(s): Huan Zhang, Asim Ali, Jianing Gao, Rongjun Ban, Xiaohua Jiang, Yuanwei Zhang, Qinghua Shi
Software Mentions: 1
Published: over 8 years ago

10.1093/database/bav022

Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer
Cited by: 4
Author(s): Ji Hyun Lee, Sungyong You, Do Young Hyeon, Byeongsoo Kang, Hyerim Kim, Kyoung Mii Park, Byung-Woo Han, Daehee Hwang, Sung Hoon Kim
Software Mentions: 1
Published: over 11 years ago

10.1093/database/bat074

HypoxiaDB: a database of hypoxia-regulated proteins
Cited by: 29
Author(s): Pankaj Khurana, R. Sugadev, Jaspreet Jain, Shashi Bala Singh
Software Mentions: 1
Published: over 13 years ago

10.1093/database/baaa073

A curated database reveals trends in single-cell transcriptomics
Cited by: 130
Author(s): Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter
Software Mentions: 1
Published: over 6 years ago

10.1016/j.devcel.2016.10.015

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances
Cited by: 188
Author(s): Orsolya Symmons, Leslie Pan, Silvia Remeseiro, Tuğçe Aktaş, Felix A. Klein, Wolfgang Huber, François Spitz
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms21103480

The GOLIATH Project: Towards an Internationally Harmonised Approach for Testing Metabolism Disrupting Compounds
Cited by: 33
Author(s): Juliette Legler, Daniel Zalko, Fabien Jourdan, Miriam N. Jacobs, Bernard Fromenty, Patrick Balaguer, William Bourguet, Vesna Munić Kos, Ángel Nadal, Claire Beausoleil, Susana Cristóbal, Sylvie Remy, Sibylle Ermler, Luigi Margiotta-Casaluci, Julian L. Griffin, Bruce Blumberg, Christophe Chesné, Sebastian Hoffmann, Patrik L. Andersson, Jorke H. Kamstra
Software Mentions: 1
Published: over 6 years ago

10.1016/j.devcel.2014.12.024

Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State
Cited by: 70
Author(s): Shilu Amin, Ian J. Donaldson, Denise A. Zannino, James Hensman, Magnus Rattray, Marta Losa, François Spitz, Franck Ladam, Charles G. Sagerström, Nicoletta Bobola
Software Mentions: 1
Published: over 11 years ago

10.1242/dev.168146

Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes
Cited by: 17
Author(s): Toru Suzuki, Chisato Kikuguchi, Saori Nishijima, Takeshi Nagashima, Akinori Takahashi, Mariko Okada, Tadashi Yamamoto
Software Mentions: 1
Published: over 7 years ago

10.1242/dev.112623

Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation <i>in vivo</i>
Cited by: 53
Author(s): Isabel Olivera-Martínez, Nicholas J. Schurch, Roman A. Li, Junfang Song, Pamela A. Halley, Raman M Das, David W. Burt, Geoffrey J. Barton, Kate G. Storey
Software Mentions: 1
Published: about 12 years ago

10.1242/dmm.021626

Pulmonary transcriptome analysis in the rabbit model of surgically-induced diaphragmatic hernia treated with fetal tracheal occlusion
Cited by: 17
Author(s): Alexander C. Engels, Paul Brady, Molka Kammoun, Julio Finalet Ferreiro, Philip DeKoninck, Masayuki Endo, Jaan Toelen, Joris Robert Vermeesch, Jan Deprest
Software Mentions: 1
Published: over 10 years ago

10.1016/j.drudis.2012.07.014

Transcriptional data: a new gateway to drug repositioning?
Cited by: 193
Author(s): Francesco Iorio, Timothy Rittman, Hong Ge, Michael P. Menden, Julio Sáez-Rodríguez
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0030781

Circadian Rhythms of Fetal Liver Transcription Persist in the Absence of Canonical Circadian Clock Gene Expression Rhythms In Vivo
Cited by: 8
Author(s): Chengwei Li, Shuang Yu, Xiaoling Zhong, Jianguo Wu, Xiaodong Li
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0106278

SDF-1 Chemokine Signalling Modulates the Apoptotic Responses to Iron Deprivation of Clathrin-Depleted DT40 Cells
Cited by: 2
Author(s): Alena Pance, Frank Ralf Morrissey-Wettey, Helen Craig, Alison Downing, Richard Talbot, Antony P. Jackson
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0082684

Genetic Interaction between Mutations in c-Myb and the KIX Domains of CBP and p300 Affects Multiple Blood Cell Lineages and Influences Both Gene Activation and Repression
Cited by: 27
Author(s): Lawryn H. Kasper, Tsutomu Fükuyama, Stephanie Lerach, Yunchao Chang, Wu Xu, Song Wu, Kelli L. Boyd, Paul K. Brindle
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms21113749

17-Aminogeldanamycin Inhibits Constitutive Nuclear Factor-Kappa B (NF-κB) Activity in Patient-Derived Melanoma Cell Lines
Cited by: 7
Author(s): Mariusz L. Hartman, Magdalena Rogut, Aleksandra Mielczarek-Lewandowska, Michal Wozniak, Małgorzata Czyż
Software Mentions: 1
Published: about 6 years ago

10.15252/emmm.201708163

An <scp>FGFR</scp> 3/ <scp>MYC</scp> positive feedback loop provides new opportunities for targeted therapies in bladder cancers
Cited by: 40
Author(s): Mélanie Mahé, Florent Dufour, Hélène Neyret–Kahn, Aura Ileana Moreno-Vega, C Béraud, Ming Shi, Iméne Hamaidi, Virginia Sánchez-Quiles, Clémentine Krucker, Marion Dorland‐Galliot, Élodie Chapeaublanc, Rémy Nicolle, Hervé Lang, Célio Pouponnot, Thierry Massfelder, François Radvanyi, Isabelle Bernard‐Pierrot
Software Mentions: 1
Published: over 8 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962