bioconductor: ArrayExpress | Projects

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.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.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.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

10.1371/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.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

10.1186/s13023-014-0160-2

Molecular characterization of subcutaneous panniculitis-like T-cell lymphoma reveals upregulation of immunosuppression- and autoimmunity-associated genes
Cited by: 15
Author(s): Pilvi Maliniemi, Sonja Hahtola, Kristian Ovaska, Leila Jeskanen, Liisa Väkevä, Kirsi Jäntti, Rudolf Stadler, David Michonneau, Sylvie Fraïtag, Sampsa Hautaniemi, Annamari Ranki
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0001403

Probing Host Pathogen Cross-Talk by Transcriptional Profiling of Both Mycobacterium tuberculosis and Infected Human Dendritic Cells and Macrophages
Cited by: 185
Author(s): Ludovic Tailleux, Simon J. Waddell, Mattia Pelizzola, Alessandra Mortellaro, Michael Withers, Antoine Tanne, Paola Ricciardi Castagnoli, Brigitte Gicquel, Neil G. Stoker, Philip D. Butcher, Maria Foti, Olivier Neyrolles
Software Mentions: 1
Published: over 18 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.0139446

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions
Cited by: 32
Author(s): Francesco Iorio, Roshan L. Shrestha, Nicolas Levin, Viviane Boilot, Mathew J. Garnett, Julio Sáez-Rodríguez, Viji M. Draviam
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0080047

A Small RNA Encoded in the Rv2660c Locus of Mycobacterium tuberculosis Is Induced during Starvation and Infection
Cited by: 32
Author(s): Joanna Houghton, Teresa Cortes, Olga T. Schubert, Graham Rose, Angela Rodgers, Megan De Ste Croix, Rudolf Aebersold, Douglas B. Young, Kristine B. Arnvig
Software Mentions: 1
Published: over 12 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.0113053

Toward Computational Cumulative Biology by Combining Models of Biological Datasets
Cited by: 8
Author(s): Ali Faisal, Jaakko Peltonen, Elisabeth Georgii, Johan Rung, Samuel Kaski
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0250747

Glycans unique to the relapse-prone subset within triple-negative breast cancer as revealed by lectin array-based analysis of surgical specimens
Cited by: 3
Author(s): Madoka Sakata-Matsuzawa, Kaori Denda-Nagai, Haruhiko Fujihira, Miki Noji, Katrin Ishii-Schrade, Atsushi Matsuda, Atsushi Kuno, Misato Okazaki, Keiichi Nakai, Yoshiya Horimoto, Mitsue Saito, Tatsuro Irimura
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0026023

Hormone Receptor and ERBB2 Status in Gene Expression Profiles of Human Breast Tumor Samples
Cited by: 6
Author(s): Anna Dvorkin‐Gheva, John A. Hassell
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0080747

PaGenBase: A Pattern Gene Database for the Global and Dynamic Understanding of Gene Function
Cited by: 100
Author(s): Jianbo Pan, Shichang Hu, Dan Shi, Mei-Chun Cai, Yin-Bo Li, Quan Zou, Zhi-Liang Ji
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0048363

Functional Similarities between Pigeon ‘Milk’ and Mammalian Milk: Induction of Immune Gene Expression and Modification of the Microbiota
Cited by: 28
Author(s): Meagan J Gillespie, Dragana Stanley, Honglei Chen, John A. Donald, Kevin R. Nicholas, Robert J. Moore, Tamsyn M. Crowley
Software Mentions: 1
Published: almost 14 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

10.1186/1471-2164-11-418

Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar)
Cited by: 124
Author(s): Samuel Martín, Alex Douglas, D.F. Houlihan, Christopher J. Secombes
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0001546

Systematic Validation and Atomic Force Microscopy of Non-Covalent Short Oligonucleotide Barcode Microarrays
Cited by: 13
Author(s): Michael A. Cook, Chi Kin Chan, Paul Jorgensen, Troy Ketela, Daniel K. C. So, Mike Tyers, Chi Yip Ho
Software Mentions: 1
Published: over 18 years ago

10.1186/ar3069

Gene expression profiling in circulating endothelial cells from systemic sclerosis patients shows an altered control of apoptosis and angiogenesis that is modified by iloprost infusion
Cited by: 19
Author(s): Elisa Tinazzi, Marzia Dolcino, Antonio Puccetti, Antonella Rigo, Ruggero Beri, Maria Teresa Valenti, Roberto Corrocher, Claudio Lunardi
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0079627

Integrative Analysis of mRNA Expression and Half-Life Data Reveals Trans-Acting Genetic Variants Associated with Increased Expression of Stable Transcripts
Cited by: 1
Author(s): Thong Tien Nguyen, Cathal Seoighe
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0161993

PKC-ALDH2 Pathway Plays a Novel Role in Adipocyte Differentiation
Cited by: 20
Author(s): Yu-Hsiang Yu, Pei Ru Liao, Chien Jung Guo, Che Hong Chen, Daria Mochly‐Rosen, Lee‐Ming Chuang
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0008018

Sulfur Metabolism Actively Promotes Initiation of Cell Division in Yeast
Cited by: 17
Author(s): Heidi M. Blank, Shefali Rajendra Gajjar, Andrey Belyanin, Michael Polymenis
Software Mentions: 1
Published: over 16 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: almost 9 years ago

10.1186/s12864-019-5464-0

A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes
Cited by: 3
Author(s): Marzena Mura, Roman Jaksik, Anna Lalik, Krzysztof Biernacki, Marek Kimmel, Joanna Rzeszowska-Wolny, Krzysztof Fujarewicz
Software Mentions: 1
Published: over 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.0002798

Diurnal and Circadian Rhythms in the Tomato Transcriptome and Their Modulation by Cryptochrome Photoreceptors
Cited by: 63
Author(s): Paolo Facella, Loredana Lopez, Fabrizio Carbone, David W. Galbraith, Giovanni Giuliano, Gaetano Perrotta
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0184087

SEXCMD: Development and validation of sex marker sequences for whole-exome/genome and RNA sequencing
Cited by: 7
Author(s): Seongmun Jeong, Ji-Woong Kim, Won Park, Hongmin Jeon, Namshin Kim
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-7-319

Systematic interpretation of microarray data using experiment annotations
Cited by: 17
Author(s): Kurt Fellenberg, Christian Busold, Olaf Witt, Andrea S. Bauer, Boris Beckmann, Nicole Hauser, Marcus Frohme, Stefan Winter, Jürgen Dippon, Jörg D. Hoheisel
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pone.0131336

MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing
Cited by: 29
Author(s): Li Zhang, Pengfei Wei, Xudong Shen, Yuanwei Zhang, Bo Xu, Jun Zhou, Song Fan, Zongyao Hao, Hao Shi, Xiansheng Zhang, Rui Kong, Lingfan Xu, Duohong Zou, Chaozhao Liang
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-9-3

Switch-like genes populate cell communication pathways and are enriched for extracellular proteins
Cited by: 36
Author(s): Adam Ertel, Aydın Tözeren
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0070294

Prediction Errors in Learning Drug Response from Gene Expression Data – Influence of Labeling, Sample Size, and Machine Learning Algorithm
Cited by: 15
Author(s): Immanuel Bayer, Philip Groth, Sebastian Schneckener
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-8-202

Species differences in brain gene expression profiles associated with adult behavioral maturation in honey bees
Cited by: 48
Author(s): Moushumi Sen Sarma, Charles W. Whitfield, Gene E. Robinson
Software Mentions: 1
Published: over 19 years ago

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

10.3390/ijms22126505

Screen Key Genes Associated with Distraction-Induced Osteogenesis of Stem Cells Using Bioinformatics Methods
Cited by: 2
Author(s): Jishizhan Chen, Jia Hua, Wenhui Song
Software Mentions: 1
Published: about 5 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

10.1186/2051-5960-2-23

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: over 12 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/s41598-018-21915-8

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 8 years ago

10.1186/1471-2164-14-169

Transcriptome analysis of pigeon milk production – role of cornification and triglyceride synthesis genes
Cited by: 38
Author(s): Meagan J Gillespie, Tamsyn M. Crowley, Volker Häring, Susanne Wilson, Jennifer Harper, Jean Payne, Diane Green, Paul Monaghan, John A. Donald, Kevin R. Nicholas, Robert J. Moore
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0048896

Survival of Staphylococcus aureus ST398 in the Human Nose after Artificial Inoculation
Cited by: 23
Author(s): Bibi C. G. C. Slingerland, Mehri Tavakol, Alex J. McCarthy, Jodi A. Lindsay, Susan V. Snijders, Jaap A. Wagenaar, Alex van Belkum, Margreet C. Vos, Henri A. Verbrugh, Willem J. B. van Wamel
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0152786

Adipocytes as a Link Between Gut Microbiota-Derived Flagellin and Hepatocyte Fat Accumulation
Cited by: 13
Author(s): Eveliina Munukka, Petri Wiklund, Tiina Partanen, Sakari Välimäki, Eija K. Laakkonen, Maarit Lehti, Pamela Fischer-Posovzsky, Martin Wabitsch, Sulin Cheng, Pentti Huovinen, Satu Pekkala
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0007158

miR-155 Inhibition Sensitizes CD4+ Th Cells for TREG Mediated Suppression
Cited by: 81
Author(s): Heiko Stahl, Tanja Fauti, Nina D. Ullrich, Tobias Bopp, Jan Kubach, Werner Rust, Paul Labhart, Vassili Alexiadis, Christian Becker, Mathias Hafner, Andreas Weith, Martin Lenter, Helmut Jonuleit, Edgar Schmitt, Detlev Mennerich
Software Mentions: 1
Published: almost 17 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 8 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

10.1038/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 8 years ago

10.1186/1471-2164-8-181

Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni
Cited by: 34
Author(s): Michael Waisberg, Francisco Pereira Lobo, Gustavo C. Cerqueira, Liana Konovaloff Jannotti Passos, Omar S. Carvalho, Glória Regina Franco, Najib M. El-Sayed
Software Mentions: 1
Published: over 19 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

10.1186/1471-2164-8-387

BMDExpress: a software tool for the benchmark dose analyses of genomic data
Cited by: 160
Author(s): Longlong Yang, Bruce C. Allen, Russell S. Thomas
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pone.0073072

Transmembrane Prostatic Acid Phosphatase (TMPAP) Interacts with Snapin and Deficient Mice Develop Prostate Adenocarcinoma
Cited by: 27
Author(s): Ileana B. Quintero, Annakaisa Herrala, César L. Araujo, Anitta E. Pulkka, Sampsa Hautaniemi, Kristian Ovaska, Evgeny Pryazhnikov, Evgeny Kulesskiy, Maija Ruuth, Ylermi Soini, Raija Sormunen, Leonard Khirug, Pirkko Vihko
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0045200

Transcriptomic Assay of CD8+ T Cells in Treatment-Naïve HIV, HCV-Mono-Infected and HIV/HCV-Co-Infected Chinese
Cited by: 7
Author(s): Jin Zhao, Yi Liu, Jing Lu, Zheng Yang, Ying Chen, Chenli Zheng, Dan Huang, Yufeng Li, Lin Chen, Jinquan Cheng, Hsiang‐Fu Kung, Ming‐Liang He
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0123342

Differential Transcriptional Profiling of Damaged and Intact Adjacent Dorsal Root Ganglia Neurons in Neuropathic Pain
Cited by: 39
Author(s): Ann-Kristin Reinhold, Laura Batti, Daniel Bilbao, Andreas Buneß, Heike L. Rittner, Paul A. Heppenstall
Software Mentions: 1
Published: over 11 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

10.1186/s12864-016-2562-0

Effects of drought and salt-stresses on gene expression in Caragana korshinskii seedlings revealed by RNA-seq
Cited by: 44
Author(s): Shaofeng Li, Chengming Fan, Yán Li, Jianhui Zhang, Jie Sun, Yuhong Chen, Tian Chen, Xiaohua Su, Mengzhu Lu, Chengzhi Liang, Zhongliang Hu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0199991

PASI: A novel pathway method to identify delicate group effects
Cited by: 4
Author(s): Maria K. Jaakkola, Aidan McGlinchey, Рику Клен, Laura L. Elo
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-018-4954-9

Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression
Cited by: 13
Author(s): Jochen T. Bick, Veronika L. Flöter, Mark D. Robinson, Stefan Bauersachs, Susanne E. Ulbrich
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0055506

Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?
Cited by: 34
Author(s): David Cohen, Marie‐Béatrice Bogeat‐Triboulot, Silvère Vialet-Chabrand, Rémy Merret, Pierre‐Emmanuel Courty, Sébastien Moretti, François Bizet, Agnès Guilliot, Irène Hummel
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0118511

MicroRNA-572 Improves Early Post-Operative Cognitive Dysfunction by Down-Regulating Neural Cell Adhesion Molecule 1
Cited by: 31
Author(s): Xiuchong Yu, Shupeng Liu, Jinbao Li, Xiaoping Fan, Yuanjie Chen, Xiaoying Bi, Shanrong Liu, Xiaoming Deng
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0049077

Gadd45α: A Novel Diabetes-Associated Gene Potentially Linking Diabetic Cardiomyopathy and Baroreflex Dysfunction
Cited by: 13
Author(s): Ning Wang, Chao Yang, Fang Xie, Lichao Sun, Xiaolin Su, Ying Wang, Ran Wei, Rong Zhang, Xia Li, Baofeng Yang, Jing Ai
Software Mentions: 1
Published: over 13 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

10.1186/1471-2164-7-113

Cross-species hybridizations on a multi-species cDNA microarray to identify evolutionarily conserved genes expressed in oocytes
Cited by: 41
Author(s): Maud Vallée, Claude Robert, S. Méthot, Marie‐France Palin, Marc‐André Sirard
Software Mentions: 1
Published: over 20 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

10.1371/journal.pone.0013079

QKI-7 Regulates Expression of Interferon-Related Genes in Human Astrocyte Glioma Cells
Cited by: 8
Author(s): Lin Jiang, Peter Saetre, Katarzyna J. Radomska, Elena Jazin, Eva Carlström
Software Mentions: 1
Published: almost 16 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.0013658

Whole Blood Transcriptomics in Cardiac Surgery Identifies a Gene Regulatory Network Connecting Ischemia Reperfusion with Systemic Inflammation
Cited by: 34
Author(s): Orfeas Liangos, Sophie Domhan, Christian Schwager, Martin Zeier, Peter E. Huber, Francesco Addabbo, Michael S. Goligorsky, Lynn Hlatky, Bertrand L. Jaber, Amir Abdollahi
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0183410

snoRNA and piRNA expression levels modified by tobacco use in women with lung adenocarcinoma
Cited by: 25
Author(s): Natasha Andressa Nogueira Jorge, Gabriel Wajnberg, Carlos Gil Ferreira, Benilton Carvalho, Fábio Passetti
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-14-301

Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis
Cited by: 53
Author(s): Victoria A Jenkins, Geraint Barton, Brian D. Robertson, Katrina Williams
Software Mentions: 1
Published: over 13 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.0009867

Oral Activated Charcoal Prevents Experimental Cerebral Malaria in Mice and in a Randomized Controlled Clinical Trial in Man Did Not Interfere with the Pharmacokinetics of Parenteral Artesunate
Cited by: 10
Author(s): J. Brian de Souza, Uduak Okomo, Alexander Nast, Naveed Aziz, Benjamin M. J. Owens, Harsimran Kaur, Momodou Jasseh, Sant Muangnoicharoen, Percy F. Sumariwalla, David C. Warhurst, Stephen A. Ward, David J. Conway, Luis Ulloa, Kevin J. Tracey, Brian M. J. Foxwell, Paul M. Kaye, Michael Walther
Software Mentions: 1
Published: over 16 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.0141710

Expression of CCL20 and Its Corresponding Receptor CCR6 Is Enhanced in Active Inflammatory Bowel Disease, and TLR3 Mediates CCL20 Expression in Colonic Epithelial Cells
Cited by: 51
Author(s): Helene Kolstad Skovdahl, Atle van Beelen Granlund, Ann Elisabet Østvik, Ingrid Bakke, Sverre Helge Torp, Jan Kristian Damås, Arne K. Sandvik
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-8-450

Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance
Cited by: 75
Author(s): Fanny Ramel, Cécile Sulmon, Francisco Cabello‐Hurtado, Ludivine Taconnat, Marie‐Laure Martin‐Magniette, Jean-Pierre Renou, Abdelhak El Amrani, Ivan Couée, Gwenola Gouesbet
Software Mentions: 1
Published: over 18 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.pone.0043249

Induction of Endoplasmic Reticulum Stress Response by the Indole-3-Carbinol Cyclic Tetrameric Derivative CTet in Human Breast Cancer Cell Lines
Cited by: 43
Author(s): Luca Galluzzi, Mauro De Santi, Rita Crinelli, Cinzia De Marco, Nadia Zaffaroni, Andrea Duranti, Giorgio Brandi, Mauro Magnani
Software Mentions: 1
Published: about 14 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.0052321

Focal DNA Copy Number Changes in Neuroblastoma Target MYCN Regulated Genes
Cited by: 37
Author(s): Candy Kumps, Annelies Fieuw, Pieter Mestdagh, Björn Menten, Steve Lefever, Filip Pattyn, Sara De Brouwer, Tom Sante, Johannes H. Schulte, Alexander Schramm, Nadine Van Roy, Tom Van Maerken, Rosa Noguera, Valérie Combaret, Christine Devalck, Frank Westermann, Geneviève Laureys, Angelika Eggert, Jo Vandesompele, Katleen De Preter, Franki Speleman
Software Mentions: 1
Published: over 13 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.pntd.0002438

Temephos Resistance in Aedes aegypti in Colombia Compromises Dengue Vector Control
Cited by: 106
Author(s): Nelson Grisales, Rodolphe Poupardin, Santiago Gómez, Idalyd Fonseca-González, Hilary Ranson, Audrey Lenhart
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-14-710

Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression
Cited by: 26
Author(s): Paul Golby, Javier Nuñez, Adam A. Witney, Jason Hinds, Michael A. Quail, Stephen D. Bentley, Simon R. Harris, Noel H. Smith, R. Glyn Hewinson, Stephen V. Gordon
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-020-6712-z

Lung transcriptomic clock predicts premature aging in cigarette smoke-exposed mice
Cited by: 12
Author(s): Mohamed-Amin Choukrallah, Julia Hoeng, Manuel C. Peitsch, Florian Martin
Software Mentions: 1
Published: over 6 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.pntd.0002607

Bioassay-Guided Fractionation of Extracts from Codiaeum variegatum against Entamoeba histolytica Discovers Compounds That Modify Expression of Ceramide Biosynthesis Related Genes
Cited by: 14
Author(s): Emmanuel Mfotie Njoya, Christian Weber, Nora Adriana Hernández‐Cuevas, Chung-Chau Hon, Yves L. Janin, Melanie F. G. Kamini, Paul Fewou Moundipa, Nancy Guillén
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pntd.0005069

Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection
Cited by: 67
Author(s): Kayvan Etebari, Sultan Asad, Guangmei Zhang, Sassan Asgari
Software Mentions: 1
Published: almost 10 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.pntd.0001692

Gene Amplification, ABC Transporters and Cytochrome P450s: Unraveling the Molecular Basis of Pyrethroid Resistance in the Dengue Vector, Aedes aegypti
Cited by: 156
Author(s): Vassiliki Bariami, Christopher M. Jones, Rodolphe Poupardin, John Vontas, Hilary Ranson
Software Mentions: 1
Published: about 14 years ago

10.1038/s41598-018-37591-7

Author Correction: Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 1
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Connor Rogerson, Christopher W. Bleaney, Andrew Cowie, Karen Pickard, Massimiliano Mellone, C Choh, Mathieu Derouet, Patrick J. Duriez, Fergus Noble, Michael J. White, John Primrose, Jonathan C. Strefford, Matthew Rose-Zerilli, Gareth J. Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C. Fitzgerald, Tim Underwood
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pntd.0005972

Next-generation ELISA diagnostic assay for Chagas Disease based on the combination of short peptidic epitopes
Cited by: 28
Author(s): Juan Mucci, Santiago J. Carmona, Romina Volcovich, Jaime Altcheh, Estefanisa Bracamonte, Jorge Diego Marco, Morten Nielsen, Carlos A. Buscaglia, Fernán Agüero
Software Mentions: 1
Published: almost 9 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

10.1038/s41598-019-42750-5

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

10.1186/s12864-017-4200-x

Genes for asparagine metabolism in Lotus japonicus: differential expression and interconnection with photorespiration
Cited by: 8
Author(s): Margarita García‐Calderón, Carmen M. Pérez-Delgado, Alfredo Credali, José M. Vega, Marco Betti, Antonio J. Márquez
Software Mentions: 1
Published: almost 9 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.pmed.1000046

A Compendium of Potential Biomarkers of Pancreatic Cancer
Cited by: 256
Author(s): H. C. Harsha, Kumaran Kandasamy, Prathibha Ranganathan, Sandhya Rani, Subhashri Ramabadran, Sashikanth Gollapudi, Lavanya Balakrishnan, Sutopa B. Dwivedi, Deepthi Telikicherla, Lakshmi Dhevi N. Selvan, Renu Goel, Suresh Mathivanan, Arivusudar Marimuthu, Manoj Kumar Kashyap, Robert F. Vizza, Robert J. Mayer, James A. DeCaprio, Sudhir Srivastava, Samir Hanash, Ralph H. Hruban, Akhilesh Pandey
Software Mentions: 1
Published: over 17 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

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962