bioconductor: ArrayExpress | Projects

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: about 11 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: about 13 years ago

10.1242/bio.047530

Forcing contacts between mitochondria and the endoplasmic reticulum extends lifespan in a <i>Drosophila</i> model of Alzheimer's disease
Cited by: 25
Author(s): Juan Garrido-Maraver, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 1
Published: about 7 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.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: over 12 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: over 10 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: over 17 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: about 16 years ago

10.1007/s00253-017-8317-2

Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris
Cited by: 25
Author(s): Rochelle Aw, Geraint Barton, David J. Leak
Software Mentions: 1
Published: over 8 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: over 9 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: about 12 years ago

10.18632/oncotarget.9379

GFOD1 and peejar are promising markers for clear-cell renal cell carcinoma disease progression
Cited by: 3
Author(s): Xiaorong Wu, Yonghui Chen, Wei Chen, Wen Kong, Jiwei Huang, Zhendong Jin, Wei Xue, Dongming Liu, Yiran Huang
Software Mentions: 1
Published: over 9 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: about 18 years ago

10.1186/1477-7827-7-133

Fhl5/Act, a CREM-binding transcriptional activator required for normal sperm maturation and morphology, is not essential for testicular gene expression
Cited by: 13
Author(s): Aurélie Lardenois, Frédéric Chalmel, Philippe Demougin, Noora Kotaja, Paolo Sassone‐Corsi, Michael Primig
Software Mentions: 1
Published: about 16 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

10.1186/1477-7827-8-154

Profiling spermatogenic failure in adult testes bearing Sox9-deficient Sertoli cells identifies genes involved in feminization, inflammation and stress
Cited by: 11
Author(s): Aurélie Lardenois, Frédéric Chalmel, Francisco Barrionuevo, Philippe Demougin, Gerd Scherer, Michael Primig
Software Mentions: 1
Published: about 15 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: over 13 years ago

10.1093/bioinformatics/btt019

CluePedia Cytoscape plugin: pathway insights using integrated experimental and <i>in silico</i> data
Cited by: 841
Author(s): Gabriela Bindea, Jérôme Galon, Bernhard Mlecnik
Software Mentions: 1
Published: about 13 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: about 12 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: almost 13 years ago

10.18632/oncotarget.9578

Functional/activity network (FAN) analysis of gene-phenotype connectivity liaised by grape polyphenol resveratrol
Cited by: 15
Author(s): Tze Chen Hsieh, Sing-Yung Wu, Dylan John Bennett, Barbara B. Doonan, Erxi Wu, Joseph M. Wu
Software Mentions: 1
Published: over 9 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: over 14 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: about 6 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: almost 5 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: about 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.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: about 11 years ago

10.1186/1742-4690-11-59

Microarray analysis reveals global modulation of endogenous retroelement transcription by microbes
Cited by: 45
Author(s): George R. Young, Bettina Mavrommatis, George Kassiotis
Software Mentions: 1
Published: over 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: about 12 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: over 10 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: about 18 years ago

10.1186/s40478-014-0093-y

Integrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases
Cited by: 80
Author(s): Matthew Li, Terry C. Burns, Alexander A. Morgan, Purvesh Khatri
Software Mentions: 1
Published: over 11 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: about 12 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: over 11 years ago

10.1186/s12284-015-0059-0

Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice
Cited by: 26
Author(s): Hinako Takehisa, Yutaka Satō, Baltazar A. Antonio, Yoshiaki Nagamura
Software Mentions: 1
Published: over 10 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: almost 14 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

10.1186/1756-0381-1-9

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

10.1186/1756-0381-4-15

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: over 14 years ago

10.3390/ijms21061941

Fighting Against Promoter DNA Hyper-Methylation: Protective Histone Modification Profiles of Stress-Resistant Intestinal Stem Cells
Cited by: 1
Author(s): Torsten Thalheim, Lydia Hopp, Maria Herberg, Susann Siebert, Christiane Kerner, Marianne Quaas, Michal R. Schweiger, Gabriela Aust, Joerg Galle
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0032150

Identification of Candidate Susceptibility and Resistance Genes of Mice Infected with Streptococcus suis Type 2
Cited by: 12
Author(s): Jie Rong, Wei Zhang, Xiaohui Wang, Hongjie Fan, Lu Chen, Huochun Yao
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0112655

Identification of Modulators of the Nuclear Receptor Peroxisome Proliferator-Activated Receptor α (PPARα) in a Mouse Liver Gene Expression Compendium
Cited by: 58
Author(s): Keiyu Oshida, Naresh Vasani, Russell S. Thomas, Dawn Applegate, Mitchell B. Rosen, Barbara D. Abbott, Christopher Lau, Grace L. Guo, Lauren M. Aleksunes, Curtis D. Klaassen, J. Christopher Corton
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0181812

Reprogramming human gallbladder cells into insulin-producing β-like cells
Cited by: 33
Author(s): Feorillo Galivo, Eric Benedetti, Yuhan Wang, Carl Pelz, Jonathan Schug, Klaus H. Kaestner, Markus Grompe
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0176353

Intracellular signaling entropy can be a biomarker for predicting the development of cervical intraepithelial neoplasia
Cited by: 4
Author(s): Masakazu Sato, Kei Kawana, Katsuyuki Adachi, Asaha Fujimoto, Midori Yoshida, Hitomi Nakamura, Hidetoshi Nishida, Tatsuo Inoue, Ayumi Taguchi, Juri Ogishima, Shuichiro Eguchi, Aki Yamashita, Kensuke Tomio, Osamu Wada-Hiraike, Katsutoshi Oda, Takeshi Nagamatsu, Yutaka Osuga, Tomoyuki Fujii
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0001973

Genomic Diversity among Beijing and non-Beijing Mycobacterium tuberculosis Isolates from Myanmar
Cited by: 20
Author(s): Ruth Stavrum, Håvard Valvatne, Trond Hellem Bø, Inge Jonassen, Jason Hinds, Philip D. Butcher, Harleen M. S. Grewal
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0116973

A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network
Cited by: 39
Author(s): Felipe Leal Valentim, S. van Mourik, David Posé, Min C. Kim, Markus Schmid, Roeland C. H. J. van Ham, Marco Busscher, Gabino F. Sánchez-Pérez, Jaap Molenaar, Gerco C. Angenent, Richard G. H. Immink, Aalt D. J. van Dijk
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0064880

The Elongation Complex Components BRD4 and MLLT3/AF9 Are Transcriptional Coactivators of Nuclear Retinoid Receptors
Cited by: 14
Author(s): Sébastien Flajollet, Christophe Rachez, Maheul Ploton, Céline Schulz, Rozenn Gallais, Raphaël Métivier, Michał Pawlak, Aymeric Leray, Al Amine Issulahi, Laurent Héliot, Bart Staels, Gilles Salbert, Philippe Lefèbvre
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0198555

The immunosuppressive face of sepsis early on intensive care unit—A large-scale microarray meta-analysis
Cited by: 29
Author(s): Dominik Schaack, Benedikt Hermann Siegler, Sandra Tamulyte, Markus Weigand, Florian Uhle
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0045744

Transcriptome Analysis of Responses to Rhodomyrtone in Methicillin-Resistant Staphylococcus aureus
Cited by: 29
Author(s): Wipawadee Sianglum, Potjanee Srimanote, Peter W. Taylor, Helena Rosado, Supayang Piyawan Voravuthikunchai
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0004285

Rapid Changes in Transcription Profiles of the Plasmodium yoelii yir Multigene Family in Clonal Populations: Lack of Epigenetic Memory?
Cited by: 25
Author(s): Deirdre Cunningham, Jannik Fonager, William Jarra, Céline Carret, Peter R. Preiser, Jean Langhorne
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0022859

Identification of Human Housekeeping Genes and Tissue-Selective Genes by Microarray Meta-Analysis
Cited by: 121
Author(s): Cheng-Wei Chang, Wei‐Chung Cheng, Chaang-Ray Chen, Wun‐Yi Shu, Min-Lung Tsai, Ching-Lung Huang, Ian C. Hsu
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0190533

Elucidation of the mechanism behind the potentiating activity of baicalin against Burkholderia cenocepacia biofilms
Cited by: 17
Author(s): Lisa Slachmuylders, Heleen Van Acker, Gilles Brackman, Andrea Saß, Filip Van Nieuwerburgh, Tom Coenye
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0042228

Loss of Abdominal Muscle in Pitx2 Mutants Associated with Altered Axial Specification of Lateral Plate Mesoderm
Cited by: 14
Author(s): Diana G. Eng, Hsiao-Yen Ma, Jun Xu, Hung-Ping Shih, Michael Groß, Chrissa Kiouss
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0051129

Identification of Putative Rhamnogalacturonan-II Specific Glycosyltransferases in Arabidopsis Using a Combination of Bioinformatics Approaches
Cited by: 16
Author(s): Aline Voxeur, Aurélie André, C. Breton, Patrice Lerouge
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0080625

MicroRNA-99 Family Members Suppress Homeobox A1 Expression in Epithelial Cells
Cited by: 33
Author(s): Dan Chen, Zujian Chen, Y. Jin, Dragan Dragas, Leitao Zhang, Barima S. Adjei, Anxun Wang, Yang Dai, Xiaofeng Zhou
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0019844

Extracellular Matrix Formation Enhances the Ability of Streptococcus pneumoniae to Cause Invasive Disease
Cited by: 60
Author(s): Claudia Trappetti, Abiodun D. Ogunniyi, Marco R. Oggioni, James C. Paton
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0228408

GLIPR1 expression is reduced in multiple myeloma but is not a tumour suppressor in mice
Cited by: 2
Author(s): Natasha Friend, Jacqueline E. Noll, Khatora S. Opperman, Kimberley C. Clark, Krzysztof M. Mrozik, Kate Vandyke, Duncan R. Hewett, Andrew C.W. Zannettino
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0230313

A 3-gene biomarker signature to predict response to taxane-based neoadjuvant chemotherapy in breast cancer
Cited by: 5
Author(s): Jim Kallarackal, Florian Bürger, S. Del Bianco, Alessandro Romualdi, Martina Schad
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0001791

Transcriptomic Analyses Reveal Novel Genes with Sexually Dimorphic Expression in the Zebrafish Gonad and Brain
Cited by: 109
Author(s): Rajini Sreenivasan, Minnie Cai, Richárd Bártfai, Xingang Wang, Alan Christoffels, László Orbán
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0087665

Genome-Wide Screening Identified That miR-134 Acts as a Metastasis Suppressor by Targeting Integrin β1 in Hepatocellular Carcinoma
Cited by: 69
Author(s): Rujing Zha, Weijie Guo, Zhenfeng Zhang, Zhaoping Qiu, Qifeng Wang, Jie Ding, Shenglin Huang, Taoyang Chen, Jianren Gu, Ming Yao, Xianghuo He
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0055764

Simultaneous Quantification of Multiple Bacteria by the BactoChip Microarray Designed to Target Species-Specific Marker Genes
Cited by: 17
Author(s): Annalisa Ballarini, Nicola Segata, Curtis Huttenhower, Olivier Jousson
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0177701

SiGNet: A signaling network data simulator to enable signaling network inference
Cited by: 7
Author(s): Elizabeth A. Coker, Costas Mitsopoulos, Paul Workman, Bissan Al‐Lazikani
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0114627

Altered MicroRNA Expression Profile in Exosomes during Osteogenic Differentiation of Human Bone Marrow-Derived Mesenchymal Stem Cells
Cited by: 184
Author(s): Jiajie Xu, Guangxiao Yang, Xiaohong Pan, Shuijun Zhang, Chen Zhao, Bin-Song Qiu, Haifeng Gu, Jian-fei Hong, Li Cao, Yu Chen, Bing Xia, Qinsheng Bi, Yaping Wang
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0171508

A distal intergenic region controls pancreatic endocrine differentiation by acting as a transcriptional enhancer and as a polycomb response element
Cited by: 12
Author(s): Joris van Arensbergen, Sébastien Dussaud, Corinne Pardanaud-Glavieux, Javier García-Hurtado, Claire Sauty, Aline Guerci, Jorge Ferrer, Philippe Ravassard
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0063296

Efferocytosis Promotes Suppressive Effects on Dendritic Cells through Prostaglandin E2 Production in the Context of Autoimmunity
Cited by: 23
Author(s): Irma Pujol‐Autonell, Rosa-Maria Ampudia, Raquel Planas, Sílvia Marín-Gallén, Jorge Carrascal, Álex Sánchez, Ana V. Marín, Manel Puig-Domingo, Ricardo Pujol-Borrell, Joan Verdaguer, Marta Vives-Pi
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0017359

The PI3K p110δ Regulates Expression of CD38 on Regulatory T Cells
Cited by: 71
Author(s): Daniel T. Patton, Marcus D. Wilson, Wendy C. Rowan, Dalya R. Soond, Klaus Okkenhaug
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0011066

Contrasting Transcriptional Responses of a Virulent and an Attenuated Strain of Mycobacterium tuberculosis Infecting Macrophages
Cited by: 43
Author(s): Alice H. Li, Simon J. Waddell, Jason Hinds, Chad A. Malloff, Manjeet Bains, Robert E. W. Hancock, Wan L. Lam, Philip D. Butcher, Richard W. Stokes
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0030960

Role of Position 627 of PB2 and the Multibasic Cleavage Site of the Hemagglutinin in the Virulence of H5N1 Avian Influenza Virus in Chickens and Ducks
Cited by: 61
Author(s): K. A. Schat, John Bingham, Jeff Butler, Li Mei Chen, Sue Lowther, Tamsyn M. Crowley, Robert J. Moore, Ruben O. Donis, John W. Lowenthal
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0112399

Protein Interaction Networks Reveal Novel Autism Risk Genes within GWAS Statistical Noise
Cited by: 15
Author(s): Catarina Correia, Guiomar Oliveira, Astrid M. Vicente
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0052232

Interaction of Salmonella Typhimurium with Dendritic Cells Derived from Pluripotent Embryonic Stem Cells
Cited by: 10
Author(s): Raffaella Rossi, Christine Hale, David Goulding, Robert Andrews, Zarah Abdellah, Paul J. Fairchild, Gordon Dougan
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0084611

TFPI1 Mediates Resistance to Doxorubicin in Breast Cancer Cells by Inducing a Hypoxic-Like Response
Cited by: 14
Author(s): Gerald F. Davies, Arnie Berg, Spike D. L. Postnikoff, Heather L. Wilson, Terra Arnason, Anthony Kusalik, Troy A. A. Harkness
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0011429

Revealing New Mouse Epicardial Cell Markers through Transcriptomics
Cited by: 59
Author(s): Lars Bochmann, Padmini Sarathchandra, Frederica Mori, Enrique Lara‐Pezzi, Domenico Lazzaro, Nadia Rosenthal
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0019077

miR-132 Mediates the Integration of Newborn Neurons into the Adult Dentate Gyrus
Cited by: 140
Author(s): Bryan W. Luikart, Ae Soon L. Bensen, Eric K. Washburn, Julia V. Perederiy, Kimmy Su, Yun Li, Steven G. Kernie, Luis F. Parada, Gary L. Westbrook
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0044206

MiR-214 Targets β-Catenin Pathway to Suppress Invasion, Stem-Like Traits and Recurrence of Human Hepatocellular Carcinoma
Cited by: 142
Author(s): Hongping Xia, London Lucien Ooi, Kam M. Hui
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0200716

Identification of serum miR-1915-3p and miR-455-3p as biomarkers for breast cancer
Cited by: 45
Author(s): Jian Guo, Chen Liu, Wei Wang, Yan Liu, Huiwen He, Chong Chen, Rong Xiang, Yunping Luo
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0014672

Estrogen-Dependent Gene Expression in the Mouse Ovary
Cited by: 9
Author(s): Seng H. Liew, Mai A. Sarraj, Ann E. Drummond, Jock K. Findlay
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0106706

Research Resources: Comparative MicroRNA Profiles in Human Corona Radiata Cells and Cumulus Oophorus Cells Detected by Next-Generation Small RNA Sequencing
Cited by: 23
Author(s): Xianhong Tong, Bo Xu, Yuan‐Wei Zhang, Yusheng Liu, Chao Ma
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0145696

Correction: Lung Transcriptomics during Protective Ventilatory Support in Sepsis-Induced Acute Lung Injury
Cited by: 3
Author(s): Marialbert Acosta‐Herrera, Fabián Lorenzo-Díaz, Maria Pino‐Yanes, Almudena Corrales, Francisco Valladares, Tilman E. Klassert, Basilio Valladares, Hortense Slevogt, Shwu‐Fan Ma, Jesús Villar, Carlos Flores
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0017259

GTI: A Novel Algorithm for Identifying Outlier Gene Expression Profiles from Integrated Microarray Datasets
Cited by: 27
Author(s): John Patrick Mpindi, Henri Sara, Saija Haapa-Paananen, Sami Kilpinen, Tommi Pisto, Elmar Bucher, K. Ojala, Kristiina Iljin, Paula Vainio, Mari Björkman, Santosh Gupta, Pekka Kohonen, Matthias Nees, Olli Kallioniemi
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0073817

Wild Type p53 Transcriptionally Represses the SALL2 Transcription Factor under Genotoxic Stress
Cited by: 10
Author(s): Carlos Farkas, Carla P. Martins, D. E. Escobar, Matías I. Hepp, David B. Donner, Ariel F. Castro, Gérard I. Evan, José L. Gutiérrez, Robert S. Warren, Roxana Pincheira
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0057329

Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)
Cited by: 116
Author(s): Neha Tiwari, Nathalie Meyer-Schaller, Phil Arnold, Helena Antoniadis, Mikhail Pachkov, Erik van Nimwegen, Gerhard Christofori
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0177278

The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.)
Cited by: 23
Author(s): Bart Verwaaijen, Daniel Wibberg, Magdalena Kröber, Anderson M. Winkler, Rita Zrenner, Hanna Bednarz, Karsten Niehaus, Rita Grosch, Alfred Pühler, Andreas Schlüter
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0062456

Age-Mediated Transcriptomic Changes in Adult Mouse Substantia Nigra
Cited by: 12
Author(s): Lin Gao, María Hidalgo-Figueroa, Luis Escudero, Juan Díaz‐Martín, José López‐Barneo, Alberto Pascual
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0008939

The Transcriptional Programme of Human Heart Valves Reveals the Natural History of Infective Endocarditis
Cited by: 29
Author(s): Marie Benoit, Franck Thuny, Yannick Le Priol, Hubert Lépidi, Sonia Bastonero, Jean‐Paul Casalta, Frédéric Collart, Christian Capo, Didier Raoult, Jean‐Louis Mège
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0020063

Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
Cited by: 72
Author(s): Masayuki Murata, Hiroko Fujimoto, Kaori Nishimura, Kannikar Charoensuk, Hiroshi Nagamitsu, Satish Raina, Tomoyuki Kosaka, Taku Oshima, Nagahisa Ogasawara, Mamoru Yamada
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0109978

Life without Oxygen: Gene Regulatory Responses of the Crucian Carp (Carassius carassius) Heart Subjected to Chronic Anoxia
Cited by: 11
Author(s): Kåre‐Olav Stensløkken, Stian Ellefsen, Olga Vasieva, Yongxiang Fang, Anthony P. Farrell, Lisa Olohan, Jarle Vaage, Göran Nilsson, Andrew R. Cossins
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0053478

Genome-Wide Alteration of Histone H3K9 Acetylation Pattern in Mouse Offspring Prenatally Exposed to Arsenic
Cited by: 83
Author(s): Andrea A. Cronican, Nicholas F. Fitz, Alexis B. Carter, Muzamil Saleem, Sruti Shiva, Aaron Barchowsky, Radosveta Koldamova, Jonathan Schug, Iliya Lefterov
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0109745

Mg2+ Effect on Argonaute and RNA Duplex by Molecular Dynamics and Bioinformatics Implications
Cited by: 9
Author(s): Seungyoon Nam, Hyojung Ryu, Won Son, Yon Hui Kim, Young Ho Kim, Curt Balch, Kenneth P. Nephew, Jinhyuk Lee
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0181231

CSmiRTar: Condition-Specific microRNA targets database
Cited by: 20
Author(s): Wei Wu, Bor Wen Tu, Tsung Te Chen, Shang Wei Hou, Joseph T. Tseng
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0054717

Global Transcriptional Profiling of Longitudinal Clinical Isolates of Mycobacterium tuberculosis Exhibiting Rapid Accumulation of Drug Resistance
Cited by: 43
Author(s): Anirvan Chatterjee, Dhananjaya Saranath, Purva Bhatter, Nerges Mistry
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0089318

Global Meta-Analysis of Transcriptomics Studies
Cited by: 11
Author(s): José Caldas, Susana Vinga
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0037646

Stromal Genes Add Prognostic Information to Proliferation and Histoclinical Markers: A Basis for the Next Generation of Breast Cancer Gene Signatures
Cited by: 17
Author(s): Dwain Mefford, Joel Mefford
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0084428

DACH1: Its Role as a Classifier of Long Term Good Prognosis in Luminal Breast Cancer
Cited by: 24
Author(s): Desmond G. Powe, Gopal Krishna Dhondalay, Christophe Lemetre, Tony Allen, Hany Onsy Habashy, Ian O. Ellis, Robert C. Rees, Graham Ball
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0067802

Insulin Receptor-Overexpressing β-Cells Ameliorate Hyperglycemia in Diabetic Rats through Wnt Signaling Activation
Cited by: 14
Author(s): Mi‐Hyun Kim, Seung-Hyun Hong, Moon‐Kyu Lee
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0006576

Genome-Scale Identification Method Applied to Find Cryptic Aminoglycoside Resistance Genes in Pseudomonas aeruginosa
Cited by: 17
Author(s): Julie M. Struble, Ryan T. Gill
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0006554

Genome-Wide Profile of Pleural Mesothelioma versus Parietal and Visceral Pleura: The Emerging Gene Portrait of the Mesothelioma Phenotype
Cited by: 63
Author(s): Oluf Dimitri Røe, Endre Anderssen, E. Helge, Caroline Hild Pettersen, Anja Olsen, Helmut Sandeck, Rune Haaverstad, Steinar Lundgren, Erik G. Larsson
Software Mentions: 1
Published: over 16 years ago

10.1371/annotation/121b04a1-0cbb-4e24-8a63-fc9cdd31ec76

Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)
Cited by: 24
Author(s): Neha Tiwari, Nathalie Meyer-Schaller, Phil Arnold, Helena Antoniadis, Mikhail Pachkov, Erik van Nimwegen, Gerhard Christofori
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0218934

Ticagrelor induces paraoxonase-1 (PON1) and better protects hypercholesterolemic mice against atherosclerosis compared to clopidogrel
Cited by: 10
Author(s): Hasseri Halim, Decha Pinkaew, Preedakorn Chunhacha, Patuma Sinthujaroen, Perumal Thiagarajan, Kenichi Fujise
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0065034

Cholecalciferol (Vitamin D3) Improves Myelination and Recovery after Nerve Injury
Cited by: 102
Author(s): Jean-François Chabas, Delphine Stephan, Tanguy Marqueste, Stéphane García, Marie‐Noëlle Lavaut, Catherine Nguyen, R. Legré, Michel Khrestchatisky, Patrick Decherchi, François Féron
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0030269

Angiogenic mRNA and microRNA Gene Expression Signature Predicts a Novel Subtype of Serous Ovarian Cancer
Cited by: 99
Author(s): Stefan Bentink, Benjamin Haibe‐Kains, Thomas S. Risch, Jian–Bing Fan, Michelle S. Hirsch, Kristina M. Holton, Renee Rubio, Craig April, Jing Chen, Eliza Wickham-Garcia, Joyce F. Liu, Aedín C. Culhane, Ronny Drapkin, John Quackenbush, Ursula A. Matulonis
Software Mentions: 1
Published: almost 14 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962