bioconductor: ArrayExpress | Projects

10.1371/journal.pone.0148308

Disruption of STAT5b-Regulated Sexual Dimorphism of the Liver Transcriptome by Diverse Factors Is a Common Event
Cited by: 41
Author(s): Keiyu Oshida, Naresh Vasani, David J. Waxman, J. Christopher Corton
Software Mentions: 1
Published: over 10 years ago

10.1136/thoraxjnl-2019-213200

Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1
Cited by: 14
Author(s): C. A. Brandsma, Victor Guryev, Wim Timens, Ana Ciconelle, Dirkje S. Postma, Rainer Bischoff, Martin Johansson, Ekaterina S. Ovchinnikova, Johan Malm, György Markó-Varga, Thomas E. Fehniger, Maarten van den Berge, Péter Horvatovich
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.tranon.2021.101132

ViBiBa: Virtual BioBanking for the DETECT multicenter trial program - decentralized storage and processing
Cited by: 0
Author(s): Hannah Asperger, Jan-Philipp Cieslik, Barbara Alberter, Cäcilia Köstler, Bernhard Polzer, Volkmar Müller, Klaus Pantel, Sabine Riethdorf, André Koch, Andreas D. Hartkopf, Lisa Wiesmüller, Wolfgang Janni, Fabienne Schochter, A Franken, Dieter Niederacher, Tanja Fehm, Hans Neubauer
Software Mentions: 1
Published: about 5 years ago

10.1016/j.trecan.2020.10.011

Expanding and Remixing the Metadata Landscape
Cited by: 5
Author(s): Ariel A. Hippen, Casey S. Greene
Software Mentions: 1
Published: over 5 years ago

10.1016/j.tube.2012.12.003

Adenylylation of mycobacterial Glnk (PII) protein is induced by nitrogen limitation
Cited by: 11
Author(s): Katrina Williams, Mark H. Bennett, Geraint Barton, Victoria A Jenkins, Brian D. Robertson
Software Mentions: 1
Published: over 13 years ago

10.1016/j.tube.2013.05.004

Overexpression of the Rv0805 phosphodiesterase elicits a cAMP-independent transcriptional response
Cited by: 12
Author(s): Nishad Matange, Debbie M. Hunt, Roger S. Buxton, Sandhya S. Visweswariah
Software Mentions: 1
Published: about 13 years ago

10.1016/j.tube.2013.05.005

Characterisation of the Mycobacterium tuberculosis alternative sigma factor SigG: Its operon and regulon
Cited by: 14
Author(s): Alison Gaudion, Lisa F. Dawson, E. A. Davis, Katherine Smollett
Software Mentions: 1
Published: about 13 years ago

10.4274/tjh.2015.0145

Expression Profiles of the Individual Genes Corresponding to the Genes Generated by Cytotoxicity Experiments with Bortezomib in Multiple Myeloma
Cited by: 3
Author(s): Mehdi Ghasemi, Semih Alpsoy, Seyhan Türk, Ümi̇t Yavuz Malkan, Şükrü Atakan, İbrahim C. Haznedaroğlu, Gülsen Güneş, Mehmet Gündüz, Burak Yılmaz, Sezgin Etgül, Seda Aydın, Tuncay Aslan, Nilgün Sayınalp, Salih Aksu, Halûk Demiroğlu, Osman Özcebe, Yahya Büyükaşık, Hakan Göker
Software Mentions: 1
Published: almost 10 years ago

10.1128/mBio.01334-14

Mechanisms Underlying the Exquisite Sensitivity of Candida albicans to Combinatorial Cationic and Oxidative Stress That Enhances the Potent Fungicidal Activity of Phagocytes
Cited by: 63
Author(s): Despoina Kaloriti, Martin Jacobsen, Zhikang Yin, Miranda Patterson, Anna Tillmann, Deborah A. Smith, Emily A. Cook, Tao You, Melissa Grimm, Iryna Bohovych, Celso Grebogi, Brahm H. Segal, Neil A. R. Gow, Ken Haynes, Janet Quinn, Alistair J. P. Brown
Software Mentions: 1
Published: about 12 years ago

10.1128/mBio.00430-16

The Acinetobacter baumannii Two-Component System AdeRS Regulates Genes Required for Multidrug Efflux, Biofilm Formation, and Virulence in a Strain-Specific Manner
Cited by: 95
Author(s): Grace E. Richmond, Laura P. Evans, Michael Anderson, Matthew E. Wand, Laura C. Bonney, Alasdair Ivens, Kim Lee Chua, Mark A. Webber, J. Mark Sutton, Marnie L. Peterson, Laura J. V. Piddock
Software Mentions: 1
Published: over 10 years ago

10.1128/mBio.00642-16

DamX Controls Reversible Cell Morphology Switching in Uropathogenic Escherichia coli
Cited by: 43
Author(s): Surabhi Khandige, Cecilie Antoinette Asferg, Karina Juhl Rasmussen, Martin Jakob Larsen, Martin Overgaard, Thomas Emil Andersen, Jakob Møller‐Jensen
Software Mentions: 1
Published: about 10 years ago

10.1128/mBio.00968-17

Lack of AcrB Efflux Function Confers Loss of Virulence on <i>Salmonella enterica</i> Serovar Typhimurium
Cited by: 92
Author(s): Xuan Wang-Kan, Jessica M A Blair, Barbara Chirullo, Jonathan W. Betts, Roberto M. La Ragione, Alasdair Ivens, Vito Ricci, Timothy J. Opperman, Laura J. V. Piddock
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0041683

Identification of Novel Markers of Mouse Fetal Ovary Development
Cited by: 43
Author(s): Huijun Chen, Jodie Palmer, Rathi D Thiagarajan, Marcel E. Dinger, Emmanuelle Lesieur, Hansheng Sheng Chiu, Alexandra Schulz, Cassy M. Spiller, Sean M. Grimmond, Melissa H. Little, Peter Koopman, Dagmar Wilhelm
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0012667

Claudin 13, a Member of the Claudin Family Regulated in Mouse Stress Induced Erythropoiesis
Cited by: 16
Author(s): Pamela Thompson, Hannah Tipney, Andy Brass, Harry Noyes, Stephen J. Kemp, Jan Naessens, May Tassabehji
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0086643

Transcriptomic Meta-Analysis of Multiple Sclerosis and Its Experimental Models
Cited by: 27
Author(s): Barbara B. Raddatz, Florian Hansmann, Ingo Spitzbarth, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0075290

Coordinated and Interactive Expression of Genes of Lipid Metabolism and Inflammation in Adipose Tissue and Liver during Metabolic Overload
Cited by: 22
Author(s): Wen Miin Liang, Giulia Tonini, Petra Mulder, Thomas Kelder, Marjan van Erk, Anita M. van den Hoek, Rob Mariman, Peter Y. Wielinga, Michela Baccini, Teake Kooistra, Annibale Biggeri, Robert Kleemann
Software Mentions: 1
Published: about 13 years ago

10.1128/mBio.00109-21

Metabolomics Reveal Potential Natural Substrates of AcrB in Escherichia coli and Salmonella enterica Serovar Typhimurium
Cited by: 14
Author(s): Xuan Wang-Kan, Giovanny Rodrı́guez-Blanco, Andrew D. Southam, Catherine Winder, Warwick B. Dunn, Alasdair Ivens, Laura J. V. Piddock
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0148936

Expression of cagA, virB/D Complex and/or vacA Genes in Helicobacter pylori Strains Originating from Patients with Gastric Diseases
Cited by: 7
Author(s): Andrzej Szkaradkiewicz, Tomasz M. Karpiński, Krzysztof Linke, Przemysław Majewski, Dorota I. Rożkiewicz, Olga Goślińska-Kuźniarek
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0063210

Characterization and Comparison of 2 Distinct Epidemic Community-Associated Methicillin-Resistant Staphylococcus aureus Clones of ST59 Lineage
Cited by: 49
Author(s): Chih‐Jung Chen, Clemens Unger, W. H. Hoffmann, Jodi A. Lindsay, Yhu-Chering Huang, Friedrich Götz
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0103618

Gene Expression Analysis Suggests Bone Development-Related Genes GDF5 and DIO2 Are Involved in the Development of Kashin-Beck Disease in Children Rather than Adults
Cited by: 10
Author(s): Yan Wen, Na Zhang, Chunyan Li, Shulan He, Wenfeng Tan, Yanxia Lei, Zhang Qiang, Yu Sun, Jingjing Zheng, Xiong Guo
Software Mentions: 1
Published: about 12 years ago

10.7554/eLife.03743

The transcription factor Pitx2 positions the embryonic axis and regulates twinning
Cited by: 33
Author(s): Angela Torlopp, Mohsin A.F. Khan, Nidia M M Oliveira, Ingrid Lekk, Luz Mayela Soto‐Jiménez, Alona Sosinsky, Claudio D. Stern
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0099822

Underpinning Sustainable Vector Control through Informed Insecticide Resistance Management
Cited by: 50
Author(s): Edward Thomsen, Clare Strode, Kay Hemmings, Angela Hughes, Emmanuel Chanda, Mulenga Musapa, Mulakwa Kamuliwo, Faustina N. Phiri, Lucy Muzia, Javan Chanda, Alister Kandyata, Brian Chirwa, Kathleen Poer, Janet Hemingway, Charles S. Wondji, Hilary Ranson, Michael Coleman
Software Mentions: 1
Published: over 12 years ago

10.7554/eLife.09886

Protein kinase C coordinates histone H3 phosphorylation and acetylation
Cited by: 13
Author(s): Zoulfia Darieva, Aaron Webber, Stacey Warwood, Andrew D. Sharrocks
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0023944

A Stratified Transcriptomics Analysis of Polygenic Fat and Lean Mouse Adipose Tissues Identifies Novel Candidate Obesity Genes
Cited by: 45
Author(s): Nicholas M. Morton, Yvonne B. Nelson, Zoi Michailidou, Emma M. Di Rollo, Lynne Ramage, Patrick W. F. Hadoke, Jonathan R. Seckl, L. Bünger, Simon Horvat, Christopher J. Kenyon, Donald R. Dunbar
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0116404

Protein Interactome of Muscle Invasive Bladder Cancer
Cited by: 12
Author(s): Akshay Bhat, Andreas Heinzel, Bernd Mayer, Paul Perco, Irmgard Mühlberger, Holger Husi, Axel S. Merseburger, Jérôme Zoidakis, Antonia Vlahou, Joost P. Schanstra, Harald Mischak, Vera Jankowski
Software Mentions: 1
Published: almost 12 years ago

10.1186/s40246-020-00269-1

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

10.1371/journal.pone.0142688

Comprehensive Survey of miRNA-mRNA Interactions Reveals That Ccr7 and Cd247 (CD3 zeta) are Posttranscriptionally Controlled in Pancreas Infiltrating T Lymphocytes of Non-Obese Diabetic (NOD) Mice
Cited by: 23
Author(s): Thaís A. Fornari, Paula B. Donate, Amanda Freire Assis, Cristiana Santos de Macedo, Elza T. Sakamoto-Hojo, Eduardo Antônio Donadi, Geraldo A. S. Passos
Software Mentions: 1
Published: almost 11 years ago

10.3390/ijms10083658

Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome
Cited by: 15
Author(s): Huai-Kuang Tsai, Peiying Huang, Cheng−Yan Kao, Daryi Wang
Software Mentions: 1
Published: about 17 years ago

10.1093/hmg/ddw417

Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus
Cited by: 25
Author(s): Christopher A. Odhams, Andrea Cortini, Lingyan Chen, Amy L. Roberts, Ana Viñuela, Alfonso Buil, Kerrin S. Small, Emmanouil T. Dermitzakis, David L. Morris, Timothy J. Vyse, Deborah S. Cunninghame Graham
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0018902

Deciphering the Role of RND Efflux Transporters in Burkholderia cenocepacia
Cited by: 67
Author(s): Silvia Bazzini, Claudia Udine, Andrea Saß, Maria Rosalia Pasca, Francesca Longo, Giovanni Emiliani, Marco Fondi, Elena Perrin, Francesca Decorosi, Carlo Viti, Luciana Giovannetti, Livia Leoni, Renato Fani, Giovanna Riccardi, Eshwar Mahenthiralingam, Silvia Buroni
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0077263

Non-Specific dsRNA-Mediated Antiviral Response in the Honey Bee
Cited by: 113
Author(s): Michelle L. Flenniken, Raul Andino
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0021907

NRF2 Activation Restores Disease Related Metabolic Deficiencies in Olfactory Neurosphere-Derived Cells from Patients with Sporadic Parkinson's Disease
Cited by: 82
Author(s): Anthony Cook, Alejandra Vitale, Sugandha Ravishankar, Nicholas Matigian, Greg T. Sutherland, Jianguo Shan, Ratneswary Sutharsan, Christopher Perry, Peter A. Silburn, George D. Mellick, Murray L. Whitelaw, Christine A. Wells, Alan Mackay‐Sim, Stephen A. Wood
Software Mentions: 1
Published: over 15 years ago

10.1186/s13046-016-0403-2

Microarray-based identification of genes associated with cancer progression and prognosis in hepatocellular carcinoma
Cited by: 33
Author(s): Fuqiang Yin, Liuyang Shu, Xia Liu, Ting Li, Tao Peng, Yueli Nan, Shu Li, Xianmin Zeng, Xiaoqiang Qiu
Software Mentions: 1
Published: about 10 years ago

10.1186/s13046-016-0477-x

Nomogram integrating gene expression signatures with clinicopathological features to predict survival in operable NSCLC: a pooled analysis of 2164 patients
Cited by: 18
Author(s): Jianhui Wu, Lizhi Zhou, Lixia Huang, Jincui Gu, Shaoli Li, Baomo Liu, Jinlun Feng, Yunyun Zhou
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13046-017-0568-3

miR-500a-3p promotes cancer stem cells properties via STAT3 pathway in human hepatocellular carcinoma
Cited by: 60
Author(s): Chonghe Jiang, Jianting Long, Baoxian Liu, Ming Xu, Wei Wang, Xian-Jin Xie, Xiaolin Wang, Ming Kuang
Software Mentions: 1
Published: about 9 years ago

10.1186/s13046-017-0642-x

Drug repurposing for the treatment of glioblastoma multiforme
Cited by: 56
Author(s): Claudia Abbruzzese, Silvia Matteoni, Michele Signore, Luca Cardone, Kavindra Nath, Jerry D. Glickson, Marco G. Paggi
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13046-019-1147-6

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

10.1371/journal.pone.0038351

A Novel Strategy for Selection and Validation of Reference Genes in Dynamic Multidimensional Experimental Design in Yeast
Cited by: 49
Author(s): Ayca Cankorur-Cetinkaya, Elif Dereli, Serpil Eraslan, Muhammed Erkan Karabekmez, Duygu Dikicioglu, Betül Kırdar
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0046744

Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Brachypodium distachyon
Cited by: 89
Author(s): Lihong Chen, Wei Hu, Shenglong Tan, Min Wang, Zhanbing Ma, Shiyi Zhou, Xianwen Deng, Yang Zhang, Chao Huang, Guangxiao Yang, Guoqing He
Software Mentions: 1
Published: almost 14 years ago

10.1002/ijc.25688

Zinc deficiency activates S100A8 inflammation in the absence of COX‐2 and promotes murine oral‐esophageal tumor progression
Cited by: 37
Author(s): Shao Gui Wan, Cristian Taccioli, Yubao Jiang, Hongping Chen, Karl J. Smalley, Kun Huang, Xiu Ping Liu, John L. Farber, Carlo M. Croce, Louise Y.Y. Fong
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0070862

A Transcription Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumoniae
Cited by: 17
Author(s): Layla K. Mahdi, Esmaeil Ebrahimie, David L. Adelson, James C. Paton, Abiodun D. Ogunniyi
Software Mentions: 1
Published: about 13 years ago

10.3390/ijms11093397

Practical Application of Toxicogenomics for Profiling Toxicant-Induced Biological Perturbations
Cited by: 21
Author(s): Naoki Kiyosawa, Sunao Manabe, Takashi Yamoto, Atsushi Sanbuissho
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0074923

FHOD1, a Formin Upregulated in Epithelial-Mesenchymal Transition, Participates in Cancer Cell Migration and Invasion
Cited by: 49
Author(s): Maria Gardberg, Katja Kaipio, Laura Lehtinen, Piia Mikkonen, Vanina D. Heuser, Kati Talvinen, Kristiina Iljin, Caroline Kampf, Mathias Uhlén, Reidar Grénman, Mari Koivisto, Olli Carpén
Software Mentions: 1
Published: about 13 years ago

10.3892/ijmm.2014.2001

Integrative genomic analyses of a novel cytokine, interleukin-34 and its potential role in cancer prediction
Cited by: 30
Author(s): Bo Wang, Wei Xu, Tan Miao-lian, Xin Yan, Haiwei Yang, Tiansong Xia
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0056681

SGLT5 Reabsorbs Fructose in the Kidney but Its Deficiency Paradoxically Exacerbates Hepatic Steatosis Induced by Fructose
Cited by: 30
Author(s): Taku Fukuzawa, Motoharu Fukazawa, Otoya Ueda, Hideaki Shimada, Kito Aki, Mami Kakefuda, Yoshiaki Kawase, Naoko Wada, Chisato Goto, Naoshi Fukushima, Kou-ichi Jishage, Kazuo Honda, George L. King, Yojiro Kawabe
Software Mentions: 1
Published: over 13 years ago

10.1186/s13045-016-0339-1

The expression profile and clinic significance of the SIX family in non-small cell lung cancer
Cited by: 54
Author(s): Qian Liu, An‐Ping Li, Yijun Tian, Yu Liu, Tengfei Li, Cuntai Zhang, Jennifer D. Wu, Xinwei Han, Kongming Wu
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0153562

Competence Classification of Cumulus and Granulosa Cell Transcriptome in Embryos Matched by Morphology and Female Age
Cited by: 26
Author(s): Rehannah Borup, Lea Langhoff Thuesen, Claus Yding Andersen, Anders Nyboe-Andersen, Sören Ziebe, Ole Winther, Marie Louise Grøndahl
Software Mentions: 1
Published: over 10 years ago

10.1155/2012/984346

Cell Polarity, Epithelial-Mesenchymal Transition, and Cell-Fate Decision Gene Expression in Ductal Carcinoma In Situ
Cited by: 7
Author(s): Danila Coradini, Patrizia Boracchi, Federico Ambrogi, Elia Biganzoli, Saro Oriana
Software Mentions: 1
Published: almost 15 years ago

10.3390/ijms140611444

Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research
Cited by: 6
Author(s): Man-Wah Li, Xiaofeng Qi, Meng Ni, Hon‐Ming Lam
Software Mentions: 1
Published: over 13 years ago

10.1136/jitc-2019-000285

IL-6 promotes PD-L1 expression in monocytes and macrophages by decreasing protein tyrosine phosphatase receptor type O expression in human hepatocellular carcinoma
Cited by: 76
Author(s): Wenjie Zhang, Yang Liu, Zhongyi Yan, Hui Yang, Wei Sun, Yongliang Yao, Yun Chen, Runqiu Jiang
Software Mentions: 1
Published: over 6 years ago

10.1155/2020/8897936

SCUBE3 Is Likely a Susceptibility Gene for Systemic Lupus Erythematosus for Chinese Populations
Cited by: 2
Author(s): Yuanyuan Qi, Ya-Fei Zhao, Yunkai Zhai, Xiaoxue Zhang, Xiaoyang Wang, Xin-Ran Liu, Caixia Yan, Xianghui Ning, Zhanzheng Zhao
Software Mentions: 1
Published: almost 6 years ago

10.1155/2018/9485285

PD-L1 Expression Predicts a Distinct Prognosis in Krukenberg Tumor with Corresponding Origins
Cited by: 10
Author(s): Haiyan Tai, Qin Yang, Zhi‐Yong Wu, Sujuan Sun, Rui Cao, Yanfeng Xi, Ran Zhao, Mengyu Zhang, Zhigang Zhang, Congjian Xu
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0018088

Identification of a Gene Regulatory Network Necessary for the Initiation of Oligodendrocyte Differentiation
Cited by: 90
Author(s): Victoria A. Swiss, Tung Nguyen, Jason C. Dugas, Adiljan Ibrahim, Ben A. Barres, Ioannis P. Androulakis, Patrizia Casaccia
Software Mentions: 1
Published: over 15 years ago

10.1155/2021/7079359

Association of the PINX1 Variant rs6984094, Which Lengthens Telomeres, with Systemic Lupus Erythematosus Susceptibility in Chinese Populations
Cited by: 2
Author(s): Yuanyuan Qi, Xin-Ran Liu, HE Ying-xin, Min Zhou, Xianghui Ning, Yunkai Zhai, Xiaoxue Zhang, Xiaoyang Wang, Ya-Fei Zhao, Caixia Yan, Zhigang Zhao
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0088089

Phenotypic Modulation of Primary Vascular Smooth Muscle Cells by Short-Term Culture on Micropatterned Substrate
Cited by: 66
Author(s): Sea‐Jin Chang, Sang Yun Song, Jungsul Lee, Jonghee Yoon, Junseong Park, Sungyoung Choi, Je‐Kyun Park, Kyunghee Choi, Chulhee Choi
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0014207

Transcriptional Analysis Implicates Endoplasmic Reticulum Stress in Bovine Spongiform Encephalopathy
Cited by: 24
Author(s): Yue Tang, Wei Xiang, Linda A. Terry, Hans A. Kretzschmar, Otto Windl
Software Mentions: 1
Published: almost 16 years ago

10.1089/omi.2016.0041

Epigenomics of Total Acute Sleep Deprivation in Relation to Genome-Wide DNA Methylation Profiles and RNA Expression
Cited by: 48
Author(s): Emil Nilsson, Adrian Boström, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0031867

Human Cryptochrome-1 Confers Light Independent Biological Activity in Transgenic Drosophila Correlated with Flavin Radical Stability
Cited by: 26
Author(s): Jacqueline Vieira, Alex R. Jones, Antoine Danon, Michiyo Sakuma, Nathalie Hoang, David Robles, Shirley Tait, Derren J. Heyes, Marie Christine Picot, Taishi Yoshii, Charlotte Helfrich‐Förster, Guillaume Soubigou, Jean Yves Coppée, André Klarsfeld, François Rouyer, Nigel S. Scrutton, Margaret Ahmad
Software Mentions: 1
Published: over 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: over 6 years ago

10.3390/ijms20215274

The CCR4–NOT Deadenylase Complex Maintains Adipocyte Identity
Cited by: 11
Author(s): Akinori Takahashi, Shohei Takaoka, Shungo Kobori, Tomokazu Yamaguchi, Sara Ferwati, Keiji Kuba, Tadashi Yamamoto, Toru Suzuki
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0110288

Integrated Analysis of Microarray Data of Atherosclerotic Plaques: Modulation of the Ubiquitin-Proteasome System
Cited by: 11
Author(s): Zhe Wang, Dong Guo, Bin Yang, Jian Wang, Rong Wang, Xiaowei Wang, Qunye Zhang
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0009426

The Genome of Streptococcus mitis B6 - What Is a Commensal?
Cited by: 105
Author(s): Dalia Denapaite, Reinhold Brückner, Michael Nuhn, Peter Reichmann, Bernhard Henrich, Patrick Maurer, Yvonne Schähle, Peter Selbmann, Wolfgang Zimmermann, R. Wambutt, Regine Hakenbeck
Software Mentions: 1
Published: over 16 years ago

10.1016/j.jmb.2012.10.014

Gene Function Hypotheses for the Campylobacter jejuni Glycome Generated by a Logic-Based Approach
Cited by: 18
Author(s): Michael J.E. Sternberg, Alireza Tamaddoni‐Nezhad, Victor I. Lesk, Emily Kay, Paul G. Hitchen, Adrian P. Cootes, Lieke B. van Alphen, Marc P. Lamoureux, Harold C. Jarrell, Christopher J. Rawlings, Evelyn C. Soo, Christine M. Szymanski, Anne Dell, Brendan W. Wren, Stephen Muggleton
Software Mentions: 1
Published: almost 14 years ago

10.3390/ijms151019037

ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates
Cited by: 7
Author(s): Michael Roemer, Linus Backert, Johannes Eichner, Andreas Zell
Software Mentions: 1
Published: almost 12 years ago

10.1016/j.yjmcc.2019.02.006

The cardiomyocyte “redox rheostat”: Redox signalling via the AMPK-mTOR axis and regulation of gene and protein expression balancing survival and death
Cited by: 25
Author(s): Daniel N. Meijles, Georgia Zoumpoulidou, Thomais Markou, Kerry A Rostron, Rishi Patel, Kenneth Lay, Balvinder S. Handa, Bethany Wong, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0089297

Meta-Analysis of Pathway Enrichment: Combining Independent and Dependent Omics Data Sets
Cited by: 43
Author(s): Alexander Kaever, Manuel Landesfeind, Kirstin Feussner, Burkhard Morgenstern, Ivo Feußner, Peter Meinicke
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms20225783

Genome-Wide Identification and Characterization of ABC Transporters in Nine Rosaceae Species Identifying MdABCG28 as a Possible Cytokinin Transporter linked to Dwarfing
Cited by: 19
Author(s): Yi Feng, Qiran Sun, Guifen Zhang, Ting Wu, Xinzhong Zhang, Xuefeng Xu, Zhenhai Han, Yi Wang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0021463

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

10.7554/eLife.45051

The long non-coding RNA Cerox1 is a post transcriptional regulator of mitochondrial complex I catalytic activity
Cited by: 36
Author(s): Tamara Sirey, Kenny Roberts, Wilfried Haerty, Oscar C. Bedoya-Reina, Sebastian Rogatti-Granados, Jennifer Y. Tan, Nick Li, Lisa C. Heather, Roderick N. Carter, Sarah Cooper, Andrew J. Finch, Jimi Wills, Nicholas M. Morton, Ana C. Marques, Chris P. Ponting
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0004344

The Staphylococcus aureus Response to Unsaturated Long Chain Free Fatty Acids: Survival Mechanisms and Virulence Implications
Cited by: 157
Author(s): John Kenny, Deborah Ward, Elisabet Josefsson, Ing-Marie Jonsson, Jason Hinds, Huw H. Rees, Jodi A. Lindsay, Andrej Tarkowski, Malcolm J. Horsburgh
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0100178

Chondroitin Sulfate Proteoglycan CSPG4 as a Novel Hypoxia-Sensitive Marker in Pancreatic Tumors
Cited by: 21
Author(s): Shereen Keleg, Titov Alexandr, Anette Heller, Thomas Giese, Christine Tjaden, Sufian S. Ahmad, Matthias M. Gaida, Andrea S. Bauer, Jens Werner, Nathalia A. Giese
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0010692

Skeletal Site-Related Variation in Human Trabecular Bone Transcriptome and Signaling
Cited by: 33
Author(s): Satya S. Varanasi, Ole Kristoffer Olstad, Daniel Swan, P. L. Sanderson, Vigdis T. Gautvik, Sjur Reppe, Roger M. Francis, Kaare M. Gautvik, Harish K. Datta
Software Mentions: 1
Published: over 16 years ago

10.1186/gb-2014-15-4-r54

DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns
Cited by: 314
Author(s): Kaie Lokk, Vijayachitra Modhukur, Balaji Rajashekar, Kaspar Märtens, Reedik Mägi, Raivo Kolde, Marina Koltšina, Torbjörn Nilsson, Jaak Vilo, Andres Salumets, Neeme Tõnisson
Software Mentions: 1
Published: over 12 years ago

10.1186/gb-2013-14-12-r132

Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B
Cited by: 133
Author(s): Elinor K. Karlsson, Snaevar Sigurðsson, Emma Ivansson, Rachael Thomas, Ingegerd Elvers, Jason Wright, Cédric Howald, Noriko Tonomura, Michele Perloski, Ross Swofford, Tara Biagi, Sarah Fryc, Nathan Anderson, Céline Courtay-Cahen, Lisa Youell, Sally L. Ricketts, Sarah Mandlebaum, Patricio Rivera, Henrik von Euler, William C. Kisseberth, Cheryl A. London, Eric S. Lander, Guillermo Couto, Kenine E. Comstock, Mike Starkey, Jaime F. Modiano, Matthew Breen, Kerstin Lindblad‐Toh
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0084187

High Expression of CD109 Antigen Regulates the Phenotype of Cancer Stem-Like Cells/Cancer-Initiating Cells in the Novel Epithelioid Sarcoma Cell Line ESX and Is Related to Poor Prognosis of Soft Tissue Sarcoma
Cited by: 53
Author(s): Makoto Emori, Tomohide Tsukahara, Masaki Murase, Masanobu Kano, Kenji Murata, Akiko Takahashi, Terufumi Kubo, Hiroko Asanuma, Kazuyo Yasuda, Vitaly Kochin, Mitsunori Kaya, Satoshi Nagoya, Jun Nishio, Hiroshi Iwasaki, Tomoko Sonoda, Tadashi Hasegawa, Toshihiko Torigoe, Takuro Wada, Toshihiko Yamashita, Noriyuki Sato
Software Mentions: 1
Published: almost 13 years ago

10.1186/gb-2014-15-1-r13

Constitutive patterns of gene expression regulated by RNA-binding proteins
Cited by: 34
Author(s): Davide Cirillo, Domenica Marchese, Antonella Federico, Carmen Maria Livi, Teresa Botta-Orfila, Gian Gaetano Tartaglia
Software Mentions: 1
Published: almost 13 years ago

10.1186/gb-2013-14-6-r63

Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle
Cited by: 106
Author(s): Julietta Jupe, Remco Stam, Andrew J. M. Howden, Jenny Morris, Runxuan Zhang, Pete E. Hedley, Edgar Huitema
Software Mentions: 1
Published: over 13 years ago

10.1186/gb-2013-14-6-r65

Thermal stress effects on grain yield in Brachypodium distachyon occur via H2A.Z-nucleosomes
Cited by: 71
Author(s): Scott A. Boden, Monika Kavanová, E. Jean Finnegan, Philip A. Wigge
Software Mentions: 1
Published: over 13 years ago

10.1186/gb-2011-12-12-r127

Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera
Cited by: 31
Author(s): Tom A. Mendum, Jane Newcombe, Ahmad A. Mannan, Andrzej M. Kierzek, Johnjoe McFadden
Software Mentions: 1
Published: almost 16 years ago

10.1186/gb-2011-12-8-r82

Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast
Cited by: 39
Author(s): Brian T. Wilhelm, Samuel Marguerat, Sofia Aligianni, Sandra Codlin, Stephen Watt, Jürg Bähler
Software Mentions: 1
Published: almost 16 years ago

10.7554/eLife.69160

GIV/Girdin, a non-receptor modulator for Gαi/s, regulates spatiotemporal signaling during sperm capacitation and is required for male fertility
Cited by: 5
Author(s): Sequoyah Reynoso, Vanessa Castillo, Gajanan D. Katkar, Inmaculada López-Sánchez, Sahar Taheri, Celia R. Espinoza, Cristina C. Rohena, Debashis Sahoo, Pascal Gagneux, Pradipta Ghosh
Software Mentions: 1
Published: about 5 years ago

10.1186/gb-2011-12-6-r53

Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa
Cited by: 141
Author(s): Wei Li, Long Yan, Tai Wang
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2009-10-11-r125

High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians
Cited by: 55
Author(s): Hajime Matsuzaki, Peihua Wang, Jing Hu, Rich Rava, Glenn K. Fu
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0018796

Stroma Regulates Increased Epithelial Lateral Cell Adhesion in 3D Culture: A Role for Actin/Cadherin Dynamics
Cited by: 31
Author(s): Karen Chambers, Joanna Pearson, Naveed Aziz, Peter O’Toole, David R. Garrod, Shona Lang
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2009-10-12-r139

Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods
Cited by: 136
Author(s): Priit Adler, Raivo Kolde, Meelis Kull, Александр Георгиевич Ткаченко, Hedi Peterson, Jüri Reimand, Jaak Vilo
Software Mentions: 1
Published: almost 18 years ago

10.1186/gb-2009-10-8-r87

Depletion of T-cell intracellular antigen proteins promotes cell proliferation
Cited by: 47
Author(s): Raquel Ruz Reyes, José Alcalde, José M. Izquierdo
Software Mentions: 1
Published: almost 18 years ago

10.1186/s13059-016-0996-y

Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data
Cited by: 17
Author(s): Thomas Rensch, Diego Villar, Julie E. Horvath, Duncan T. Odom, Paul Flicek
Software Mentions: 1
Published: over 10 years ago

10.1186/gb-2008-9-5-r82

Individual mRNA expression profiles reveal the effects of specific microRNAs
Cited by: 47
Author(s): Amit Arora, David Simpson
Software Mentions: 1
Published: almost 19 years ago

10.1186/s13059-016-1064-3

Correlation of an epigenetic mitotic clock with cancer risk
Cited by: 183
Author(s): Zhen Yang, Andrew Wong, Diana Kuh, Dirk S. Paul, Vardhman K. Rakyan, Richard Leslie, Shiqing Zheng, Martin Widschwendter, Stephan Beck, Andrew E. Teschendorff
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0028552

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

10.1371/journal.pone.0040900

Distinct Genes Related to Drug Response Identified in ER Positive and ER Negative Breast Cancer Cell Lines
Cited by: 18
Author(s): Kui Shen, Shara D. Rice, David A. Gingrich, Dakun Wang, Mi Zhang, Chunqiao Tian, Zhenyu Ding, Stacey L. Brower, Paul R. Ervin, Michael J. Gabrin, George C. Tseng, Nan Song
Software Mentions: 1
Published: over 14 years ago

10.1186/gb-2004-6-1-r1

Cited by: 33
Author(s): Jeffrey G. Mandell, Jürg Bähler, Thomas A. Volpe, Robert A. Martienssen, Thomas R. Cech
Software Mentions: 1
Published: almost 23 years ago

10.3390/ijms19051369

Meta-Analysis and Experimental Validation Identified FREM2 and SPRY1 as New Glioblastoma Marker Candidates
Cited by: 11
Author(s): Marko Vidak, Ivana Jovčevska, Neja Šamec, Alja Zottel, Mirjana Liović, Damjana Rozman, Sašo Džeroski, Peter Juvan, Radovan Komel
Software Mentions: 1
Published: over 8 years ago

10.1186/gb-2008-9-1-r19

Translational control plays a prominent role in the hepatocytic differentiation of HepaRG liver progenitor cells
Cited by: 33
Author(s): Romain Parent, Laura Beretta
Software Mentions: 1
Published: almost 19 years ago

10.1186/gb-2007-8-9-r200

Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis
Cited by: 212
Author(s): Robert Kleemann, Lars Verschuren, Marjan J. van Erk, Yuri Nikolsky, N.H.P. Cnubben, Elwin Verheij, Age K. Smilde, H. Hendriks, Susanne Zadelaar, Graham J. Smith, Valery Kaznacheev, Tatiana Nikolskaya, А. С. Мельников, Eva Hurt-Camejo, J. van der Greef, Ben van Ommen, Teake Kooistra
Software Mentions: 1
Published: almost 20 years ago

10.1186/s13059-018-1472-7

Evolutionarily conserved partial gene duplication in the Triticeae tribe of grasses confers pathogen resistance
Cited by: 9
Author(s): Jeyaraman Rajaraman, Dimitar Douchkov, Stefanie Lück, Goetz Hensel, Daniela Nowara, Maria Pogoda, Twan Rutten, Tobias Meitzel, Jonathan Brassac, Caroline Höfle, Ralph Hückelhoven, Jörn Klinkenberg, Marco Trujillo, Eva Bauer, Thomas Schmutzer, Axel Himmelbach, Martin Mascher, Barbara Lazzari, Nils Stein, Jochen Kumlehn, Patrick Schweizer
Software Mentions: 1
Published: about 8 years ago

10.1186/gb-2007-8-9-r179

Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere
Cited by: 190
Author(s): Miguel A. Matilla, Manuel Espinosa‐Urgel, José J. Rodríguez‐Herva, Juan L. Ramos, Marı́a Isabel Ramos-González
Software Mentions: 1
Published: almost 20 years ago

10.1186/gb-2008-9-2-r32

Temporal regulation of expression of immediate early and second phase transcripts by endothelin-1 in cardiomyocytes
Cited by: 47
Author(s): Timothy E. Cullingford, Thomais Markou, Stephen J. Fuller, Alejandro Giraldo, Sampsa Pikkarainen, Georgia Zoumpoulidou, Ali Alsafi, Collins Ekere, Timothy J. Kemp, Jayne L. Dennis, Laurence Gamé, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: almost 19 years ago

10.1186/gb-2007-8-7-r148

Co-localization of CENP-C and CENP-H to discontinuous domains of CENP-A chromatin at human neocentromeres
Cited by: 74
Author(s): Alicia Alonso, Björn Fritz, Dan Hasson, György Abrusán, Fanny Cheung, Kinya Yoda, Bernhard Radlwimmer, Andreas G. Ladurner, Peter E. Warburton
Software Mentions: 1
Published: almost 20 years ago

10.1186/gb-2007-8-10-r229

Simplified ontologies allowing comparison of developmental mammalian gene expression
Cited by: 13
Author(s): Adéle Kruger, Oliver Hofmann, Piero Carninci, Yoshihide Hayashizaki, Winston Hide
Software Mentions: 1
Published: almost 20 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Penalties:

Papers Mentioning ArrayExpress 1,962