bioconductor: ArrayExpress | Projects

10.3389/fgene.2014.00206

Evolutionary analysis of the cystatin family in three Schistosoma species
Cited by: 13
Author(s): Yesid Cuesta-Astroz, Larissa Lopes Silva Scholte, Fabiano Sviatopolk-Mirsky Pais, Guilherme Oliveira, Laila Alves Nahum
Software Mentions: 1
Published: over 10 years ago

10.4161/rna.29196

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress
Cited by: 23
Author(s): Samuel Marguerat, Katherine Lawler, Alvis Brāzma, Jürg Bähler
Software Mentions: 1
Published: over 10 years ago

10.18632/oncotarget.6768

Inhibiting the anaphase promoting complex/cyclosome induces a metaphase arrest and cell death in multiple myeloma cells
Cited by: 33
Author(s): Susanne Lub, Anke Maes, Ken Maes, Kim De Veirman, Elke De Bruyne, Eline Menu, Karel Fostier, Alboukadel Kassambara, Jérôme Moreaux, Dirk Hose, Xavier Leleu, Randall W. King, Karin Vanderkerken, Els Van Valckenborgh
Software Mentions: 1
Published: almost 9 years ago

10.1186/1748-717X-5-25

MicroRNA expression after ionizing radiation in human endothelial cells
Cited by: 135
Author(s): Mechthild Wagner-Ecker, Christian Schwager, Ute Wirkner, Amir Abdollahi, Peter E. Huber
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0150982

A Human "eFP" Browser for Generating Gene Expression Anatograms
Cited by: 10
Author(s): Rohan Patel, Erin T. Hamanishi, Nicholas J. Provart
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0064483

Identification of Novel Tissue-Specific Genes by Analysis of Microarray Databases: A Human and Mouse Model
Cited by: 36
Author(s): Yan Song, Jinsoo Ahn, Young Ho Suh, Michael Davis, Kichoon Lee
Software Mentions: 1
Published: over 11 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: almost 15 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: almost 14 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 8 years ago

10.3389/fgene.2018.00125

Integrated Quantitative Transcriptome Maps of Human Trisomy 21 Tissues and Cells
Cited by: 32
Author(s): Maria Chiara Pelleri, Chiara Cattani, Lorenza Vitale, Francesca Antonaros, Pierluigi Strippoli, Chiara Locatelli, Guido Cocchi, Allison Piovesan, Maria Caracausi
Software Mentions: 1
Published: over 6 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 10 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 8 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 9 years ago

10.1186/1479-5876-9-72

SULFs in human neoplasia: implication as progression and prognosis factors
Cited by: 68
Author(s): Caroline Bret, Jérôme Moreaux, Jean‐François Schved, Dirk Hose, Bernard Klein
Software Mentions: 1
Published: over 13 years ago

10.18632/oncotarget.13989

Endometrial cancer cells exhibit high expression of p110β and its selective inhibition induces variable responses on PI3K signaling, cell survival and proliferation
Cited by: 14
Author(s): Thomas Karlsson, Camilla Krakstad, Ingvild L. Tangen, Erling A. Høivik, Pamela M. Pollock, Helga B. Salvesen, Aurélia E. Lewis
Software Mentions: 1
Published: almost 8 years ago

10.1038/sdata.2015.77

Comprehensive systems biology analysis of a 7-month cigarette smoke inhalation study in C57BL/6 mice
Cited by: 25
Author(s): Sam Ansari, Karine Baumer, Stéphanie Boué, Sophie Dijon, Rémi Dulize, Kim Ekroos, Ashraf Elamin, Foong Clement, Emmanuel Guedj, Julia Hoeng, Nikolai V. Ivanov, Krishnan Subash, Patrice Leroy, Florian Martin, Céline Merg, Michael J. Peck, Manuel C. Peitsch, Blaine Phillips, Walter K. Schlage, Thomas Schneider, Marja Talikka, Bjoern Titz, Patrick Vanscheeuwijck, Emilija Veljkovic, Terhi Vihervaara, Grégory Vuillaume, Ching Qing Woon
Software Mentions: 1
Published: almost 9 years ago

10.1038/sdata.2017.125

Precision annotation of digital samples in NCBI’s gene expression omnibus
Cited by: 34
Author(s): Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D. Azad, Mohamad Omar Hadied, S. Mahmood Raza, Benjamin Abhishek Rayikanti, Bin Chen, Harikrishna Paik, Dvir Aran, Jordan Spatz, Daniel S. Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A. Musen, Atul J. Butte
Software Mentions: 1
Published: about 7 years ago

10.3389/fgene.2014.00191

Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria
Cited by: 19
Author(s): Miguel A. Hernández‐Prieto, T. A. Semeniuk, Matthias E. Futschik
Software Mentions: 1
Published: over 10 years ago

10.18632/oncotarget.13414

E-cadherin downregulation sensitizes PTEN-mutant tumors to PI3Kβ silencing
Cited by: 10
Author(s): África Millán-Uclés, Susana Zuluaga, Miriam Marqués, Jesús Vallejo-Díaz, Luis Sanz, Ariel Cariaga-Martínez, Francisco X. Real, Ana C. Carrera
Software Mentions: 1
Published: about 8 years ago

10.1038/sdata.2018.29

Uniform resolution of compact identifiers for biomedical data
Cited by: 49
Author(s): Sarala M. Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A. McMurry, Niall Beard, Rafael C. Jiménez, Jeffrey S. Grethe, Henning Hermjakob, Maryann E. Martone, Tim W. Clark
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2019.00769

Inferring Latent Disease-lncRNA Associations by Faster Matrix Completion on a Heterogeneous Network
Cited by: 14
Author(s): Li Wen, Shulin Wang, Junlin Xu, Guo Mao, Geng Tian, Jialiang Yang
Software Mentions: 1
Published: about 5 years ago

10.1186/1743-7075-7-56

Identification of the Eph receptor pathway as a novel target for eicosapentaenoic acid (EPA) modification of gene expression in human colon adenocarcinoma cells (HT-29)
Cited by: 5
Author(s): Joanne F. Doleman, John J. Eady, Ruan Elliott, Robert J. Foxall, John Seers, Ian T. Johnson, Elizabeth K. Lund
Software Mentions: 1
Published: almost 15 years ago

10.3389/fgene.2014.00470

A gene mapping bottleneck in the translational route from zebrafish to human
Cited by: 2
Author(s): Nigel Klein, Mark Ibberson, Isaac Crespo, Sophie Rodius, Francisco Azuaje
Software Mentions: 1
Published: almost 10 years ago

10.1038/sdata.2019.21

The variable quality of metadata about biological samples used in biomedical experiments
Cited by: 48
Author(s): Rafael S. Gonçalves, Mark A. Musen
Software Mentions: 1
Published: almost 6 years ago

10.3389/fcell.2021.716501

GADD45B Is a Potential Diagnostic and Therapeutic Target Gene in Chemotherapy-Resistant Prostate Cancer
Cited by: 4
Author(s): Qiong Wang, Wanhua Wu, Zhe Gao, Kaiwen Li, Shirong Peng, Huiyang Fan, Zhongqiu Xie, Zhanfang Guo, Hai Huang
Software Mentions: 1
Published: over 3 years ago

10.3389/fcell.2021.673073

MeiosisOnline: A Manually Curated Database for Tracking and Predicting Genes Associated With Meiosis
Cited by: 4
Author(s): Xiaohua Jiang, Dingtao Zhao, Asim Ali, Bo Xu, Wei Liu, Jie Wen, Huan Zhang, Qinghua Shi, Yuanwei Zhang
Software Mentions: 1
Published: over 3 years ago

10.1038/s41597-019-0152-0

HENA, heterogeneous network-based data set for Alzheimer’s disease
Cited by: 33
Author(s): Elena Sügis, Jérôme Dauvillier, Anna Leontjeva, Priit Adler, Valérie Hindié, Thomas Moncion, Vincent Collura, Rachel Daudin, Yann Loe-Mie, Yann Hérault, Jean‐Charles Lambert, Henning Hermjakob, Tal Pupko, Jean-Christophe Rain, Ioannis Xénarios, Jaak Vilo, Michel Simonneau, Hedi Peterson
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0063184

Database Citation in Full Text Biomedical Articles
Cited by: 30
Author(s): Şenay Kafkas, Jee-Hyub Kim, Johanna McEntyre
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0006408

Transcriptomic Profiling of Central Nervous System Regions in Three Species of Honey Bee during Dance Communication Behavior
Cited by: 40
Author(s): Moushumi Sen Sarma, Sandra L. Rodriguez-Zas, Feng Hong, Sheng Zhong, Gene E. Robinson
Software Mentions: 1
Published: over 15 years ago

10.18632/oncotarget.16064

Integrated analysis of genes associated with poor prognosis of patients with colorectal cancer liver metastasis
Cited by: 30
Author(s): Zhenyuan Qian, Guobing Zhang, Guangyuan Song, Jing Shi, Lijie Gong, Yiping Mou, Yong Han
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0061262

The Expression of Glyceraldehyde-3-Phosphate Dehydrogenase Associated Cell Cycle (GACC) Genes Correlates with Cancer Stage and Poor Survival in Patients with Solid Tumors
Cited by: 41
Author(s): Dunrui Wang, Daniel R. Moothart, Douglas R. Lowy, Xiaolan Qian
Software Mentions: 1
Published: over 11 years ago

10.18632/oncotarget.20284

Downregulation of microRNA-31 inhibits proliferation and induces apoptosis by targeting HIF1AN in human keloid
Cited by: 21
Author(s): Juan Zhang, Dan Xu, Na Li, Yan Li, Yongjing He, Xingbo Hu, Lechun Lyu, Li He
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0065058

Retinoic Acid-Activated Ndrg1a Represses Wnt/β-catenin Signaling to Allow Xenopus Pancreas, Oesophagus, Stomach, and Duodenum Specification
Cited by: 20
Author(s): Tiejun Zhang, Xiaogang Guo, Yonglong Chen
Software Mentions: 1
Published: over 11 years ago

10.18632/oncotarget.11215

Frequency of expression and generation of T-cell responses against antigens on multiple myeloma cells in patients included in the GMMG-MM5 trial
Cited by: 5
Author(s): Michael Schmitt, Angela Hückelhoven, Michael Hundemer, Anita Schmitt, Susanne Lipp, Martina Emde, Hans Salwender, Mathias Hänel, Katja Weisel, Uta Bertsch, Jan Dürig, Anthony D. Ho, Igor Wolfgang Blau, Hartmut Goldschmidt, Anja Seckinger, Dirk Hose
Software Mentions: 1
Published: over 8 years ago

10.1038/srep15518

Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p
Cited by: 46
Author(s): Christopher J. Kershaw, Joseph L. Costello, David Talavera, William Rowe, Lydia M. Castelli, Paul F. G. Sims, Chris M. Grant, Mark P. Ashe, Simon J. Hubbard, Graham D. Pavitt
Software Mentions: 1
Published: about 9 years ago

10.18632/oncotarget.17926

Increased transcriptional and metabolic capacity for lipid metabolism in the peripheral zone of the prostate may underpin its increased susceptibility to cancer
Cited by: 11
Author(s): Omar Al Kadhi, Μαρία Τράκα, Antonietta Melchini, Perla Troncoso‐Rey, Wiktor Jurkowski, Marianne Defernez, Purnima Pachori, Robert Mills, Richard Y. Ball, Richard Mithen
Software Mentions: 1
Published: over 7 years ago

10.1186/1479-5876-8-6

Robust TLR4-induced gene expression patterns are not an accurate indicator of human immunity
Cited by: 4
Author(s): Kelly L. Brown, Reza Falsafi, Winnie W. S. Kum, Pamela Hamill, Jennifer L. Gardy, Donald J. Davidson, Stuart E. Turvey, B. Brett Finlay, David P. Speert, Robert E. W. Hancock
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0039718

Transcriptional Profiling of Serogroup B Neisseria meningitidis Growing in Human Blood: An Approach to Vaccine Antigen Discovery
Cited by: 25
Author(s): Åsa K. Hedman, Mingshi Li, Paul R. Langford, J. Simon Kroll
Software Mentions: 1
Published: over 12 years ago

10.1038/srep22989

Candida albicans repetitive elements display epigenetic diversity and plasticity
Cited by: 33
Author(s): Verónica Freire-Benéitez, R. Jordan Price, Daniel Tarrant, Judith Berman, Alessia Buscaino
Software Mentions: 1
Published: over 8 years ago

10.1038/srep23363

Exploring regulatory networks of miR-96 in the developing inner ear
Cited by: 13
Author(s): Morag A. Lewis, Annalisa Buniello, Jennifer Hilton, Fei Zhu, William I Zhang, Stephanie K. Evans, Stijn van Dongen, Anton J. Enright, Karen P. Steel
Software Mentions: 1
Published: over 8 years ago

10.1038/srep25975

A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure
Cited by: 24
Author(s): Sayak Mukhopadhyay, Ratan K. Saha, Anbarasi Palanisamy, Madhurima Ghosh, A. Biswas, Saheli Roy, Arijit Pal, Kathakali Sarkar, Sangram Bagh
Software Mentions: 1
Published: over 8 years ago

10.1038/srep26747

Intestinal APCs of the endogenous nanomineral pathway fail to express PD-L1 in Crohn’s disease
Cited by: 26
Author(s): Jack Robertson, Carolin Haas, Laetitia Pele, Tom P. Monie, Charles Charalambos, Miles Parkes, Rachel E. Hewitt, Jonathan J. Powell
Software Mentions: 1
Published: over 8 years ago

10.1038/srep27152

Hypoxia induced CCL28 promotes angiogenesis in lung adenocarcinoma by targeting CCR3 on endothelial cells
Cited by: 37
Author(s): Guichun Huang, Leilei Tao, Shihao Shen, Longbang Chen
Software Mentions: 1
Published: over 8 years ago

10.1038/srep28006

Circulating Plasma microRNAs can differentiate Human Sepsis and Systemic Inflammatory Response Syndrome (SIRS)
Cited by: 92
Author(s): Stefano Caserta, Florian Kern, Jonathan Cohen, Stephen Drage, Sarah F. Newbury, Martin J. Llewelyn
Software Mentions: 1
Published: over 8 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 5 years ago

10.1038/srep29201

Antibody-Dependent Enhancement of Dengue Virus Infection in Primary Human Macrophages; Balancing Higher Fusion against Antiviral Responses
Cited by: 95
Author(s): Jacky Flipse, Mayra Diosa-Toro, Tabitha E. Hoornweg, Denise P. I. van de Pol, Silvio Urcuqui-Inchima, Jolanda M. Smit
Software Mentions: 1
Published: over 8 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: almost 12 years ago

10.1038/srep30778

A novel human-specific splice isoform alters the critical C-terminus of Survival Motor Neuron protein
Cited by: 37
Author(s): Joonbae Seo, Natalia N. Singh, Eric W. Ottesen, Brian M. Lee, Ravindra Singh
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0009748

Cardiac Deletion of Smyd2 Is Dispensable for Mouse Heart Development
Cited by: 68
Author(s): Florian Diehl, Mark A. Brown, Machteld J. van Amerongen, Tatyana Novoyatleva, Astrid Wietelmann, June V. Harriss, Fulvia Ferrazzi, Thomas Boettger, Richard P. Harvey, Philip W. Tucker, Felix B. Engel
Software Mentions: 1
Published: over 14 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: about 13 years ago

10.1038/srep33924

Decreased IL7Rα and TdT expression underlie the skewed immunoglobulin repertoire of human B-cell precursors from fetal origin
Cited by: 17
Author(s): Magdalena B. Rother, Kristin Jensen, Mirjam van der Burg, Fleur S. van de Bovenkamp, Roel Kroek, Wilfred F. J. van IJcken, Vincent H.J. van der Velden, Tom Cupedo, Ole Kristoffer Olstad, Jacques J. M. van Dongen, Menno C. van Zelm
Software Mentions: 1
Published: about 8 years ago

10.1038/srep34730

Novel population of small tumour-initiating stem cells in the ovaries of women with borderline ovarian cancer
Cited by: 40
Author(s): Irma Virant‐Klun, Martin Štimpfel
Software Mentions: 1
Published: about 8 years ago

10.1038/srep34719

Hepatic Deletion of Janus Kinase 2 Counteracts Oxidative Stress in Mice
Cited by: 23
Author(s): Madeleine Themanns, Kristina M. Mueller, Sonja M. Kessler, Nicole Golob-Schwarzl, Thomas Mohr, Doris Kaltenecker, Jérôme Bourgeais, Jamile Paier-Pourani, Katrin Friedbichler, Doris Schneller, Michaela Schlederer, Eva Zebedin-Brandl, Luigi Terracciano, Xiaonan Han, Lukas Kenner, Kay Uwe Wagner, Wolfgang Mikulits, Andrey V. Kozlov, Markus H. Heim, Fabrice Gouilleux, Johannes Haybaeck, Richard Moriggl
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0017154

Human Primary Adipocytes Exhibit Immune Cell Function: Adipocytes Prime Inflammation Independent of Macrophages
Cited by: 170
Author(s): Kees Meijer, Marcel P. de Vries, Saad Al-Lahham, Marcel Bruinenberg, Desireé Weening, Martijn Dijkstra, Niels J. Kloosterhuis, Roelof Jan van der Leij, H van der Want, Bart-Jan Kroesen, Roel J. Vonk, Farhad Rezaee
Software Mentions: 1
Published: over 13 years ago

10.1038/srep39262

Genome-wide Analysis of WD40 Protein Family in Human
Cited by: 37
Author(s): Xudong Zou, Xue-Jia Hu, Jing Ma, Tuan Li, Zhiqiang Ye, Yun Na Wu
Software Mentions: 1
Published: almost 8 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: about 16 years ago

10.1038/srep45828

A 3q gene signature associated with triple negative breast cancer organ specific metastasis and response to neoadjuvant chemotherapy
Cited by: 19
Author(s): Jun Qian, Heidi Chen, Xiangming Ji, Rosana Eisenberg, A. Bapsi Chakravarthy, Ingrid A. Mayer, Pierre P. Massion
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0026985

Transcriptomics Responses in Marine Diatom Thalassiosira pseudonana Exposed to the Polycyclic Aromatic Hydrocarbon Benzo[a]pyrene
Cited by: 51
Author(s): Ralph Carvalho, Stephanie K. Bopp, Teresa Lettieri
Software Mentions: 1
Published: about 13 years ago

10.1038/s41598-017-01156-x

The centrosomal OFD1 protein interacts with the translation machinery and regulates the synthesis of specific targets
Cited by: 35
Author(s): Daniela Iaconis, Maria Monti, Mario Renda, Arianne van Koppen, Roberta Tammaro, Marco Chiaravalli, Flora Cozzolino, Paola Pignata, Claudia Crina, Piero Pucci, Alessandra Boletta, Vincenzo Belcastro, Rachel Giles, Enrico Maria Surace, Simone Gallo, Mario Pende, Brunella Franco
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0134866

Transcriptomic Profiling of Virus-Host Cell Interactions following Chicken Anaemia Virus (CAV) Infection in an In Vivo Model
Cited by: 19
Author(s): Efstathios S. Giotis, Lisa Rothwell, Alistair Scott, Tuanjun Hu, Richard Talbot, D. Todd, David W. Burt, Elizabeth J. Glass, Pete Kaiser
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-017-04709-2

DACH1 suppresses breast cancer as a negative regulator of CD44
Cited by: 29
Author(s): Hanxiao Xu, Shengnan Yu, Xun Yuan, Jing Xiong, Dong Kuang, Richard G. Pestell, Kongming Wu
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-05872-2

Functional and Transcriptomic Characterization of Peritoneal Immune-Modulation by Addition of Alanyl-Glutamine to Dialysis Fluid
Cited by: 12
Author(s): Rebecca Herzog, Lilian Kuster, Julia Powers Becker, Tobias Gluexam, Dietmar Pils, Andreas Spittler, Manoj Bhasin, Seth L. Alper, Andreas Vychytil, Christoph Aufricht, Klaus Kratochwill
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-06810-y

Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1
Cited by: 13
Author(s): James McCaffrey, Nicholas J.A. Webb, Toryn Poolman, Maryline Fresquet, Cressida Moxey, Leo Zeef, Ian J. Donaldson, David Ray, Rachel Lennon
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0008408

Expression Profiling the Temperature-Dependent Amphibian Response to Infection by Batrachochytrium dendrobatidis
Cited by: 144
Author(s): Laia Ribas, Mingshi Li, Benjamin J. Doddington, Jacques Robert, Judith A. Seidel, J. Simon Kroll, Lyle B. Zimmerman, Nicholas C Grassly, Trenton W. J. Garner, Matthew C. Fisher
Software Mentions: 1
Published: almost 15 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: almost 14 years ago

10.1371/journal.pone.0187920

Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization
Cited by: 15
Author(s): Thiago Jonas Nakayama, Fabiana Aparecida Rodrigues, N. Neumaier, Juliana Marcolino-Gomes, Hugo Bruno Correa Molinari, Thaís Ribeiro Santiago, Eduardo Fernandes Formighieri, Marcos Fernando Basso, J. R. B. Farias, Beatriz Marti Emygdio, A. Oliveira, Ângela Diniz Campos, Aluízio Borém, Frank G. Harmon, L. M. Mertz-Henning, Alexandre Lima Nepomuceno
Software Mentions: 1
Published: about 7 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: about 7 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 11 years ago

10.1371/journal.pone.0023466

Transcriptome Analysis of Potato Leaves Expressing the Trehalose-6-Phosphate Synthase 1 Gene of Yeast
Cited by: 31
Author(s): Mihály Kondrák, Ferenc Marincs, Balázs Kalapos, Zsófia Juhász, Zsófia Bánfalvi
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0134595

Distinct Responses of Mycobacterium smegmatis to Exposure to Low and High Levels of Hydrogen Peroxide
Cited by: 22
Author(s): Xiaojing Li, Wu Jun, Jiao Han, Yongfei Hu, Kaixia Mi
Software Mentions: 1
Published: over 9 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 9 years ago

10.18632/oncotarget.24644

MiR-21 over-expression and Programmed Cell Death 4 down-regulation features malignant pleural mesothelioma
Cited by: 12
Author(s): Lorenzo Nicolè, Rocco Cappellesso, Tiziana Sanavia, Vincenza Guzzardo, Ambrogio Fassina
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.25736

A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing’s family of tumors
Cited by: 3
Author(s): Andrew J. Annalora, Shawn T. O’Neil, Jeremy D Bushman, James Summerton, Carol S. Marcus, Patrick L. Iversen
Software Mentions: 1
Published: over 6 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 6 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 14 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 6 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 6 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: over 12 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 10 years ago

10.1371/journal.pone.0000718

An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets
Cited by: 2,166
Author(s): Deborah R. Winter, Ben Vinegar, Hardeep Nahal, Ron Ammar, Greg Wilson, Nicholas J. Provart
Software Mentions: 1
Published: over 17 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: about 9 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: over 8 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: about 12 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 10 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: almost 12 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 15 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: almost 6 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 5 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: about 7 years ago

10.18632/oncotarget.26330

Whole genome duplication is an early event leading to aneuploidy in IDH-wild type glioblastoma
Cited by: 15
Author(s): Blandine Boisselier, Frédéric Dugay, Marc‐Antoine Belaud‐Rotureau, Anne Coutolleau, Emmanuel Garcion, Philippe Meneï, Philippe Guardiola, Audrey Rousseau
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-019-43795-2

Replication termination without a replication fork trap
Cited by: 20
Author(s): Elisa Galli, Jean-Luc Ferat, Jean-Michel Desfontaines, Marie-Eve Val, Ove Skovgaard, François‐Xavier Barre, Christophe Possoz
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-46664-0

Virus Genotype-Dependent Transcriptional Alterations in Lipid Metabolism and Inflammation Pathways in the Hepatitis C Virus-infected Liver
Cited by: 18
Author(s): W. d’Avigdor, Magdalena A. Budzinska, M Lee, Roselind S. Lam, James G. Kench, Michael Stapelberg, Susan V. McLennan, Geoffrey C. Farrell, Jacob George, Geoffrey W. McCaughan, Thomas Tu, Nicholas Shackel
Software Mentions: 1
Published: over 5 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: over 5 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 8 years ago

10.1038/s41598-019-49124-x

Gene Regulatory Networks in Peripheral Mononuclear Cells Reveals Critical Regulatory Modules and Regulators of Multiple Sclerosis
Cited by: 8
Author(s): Perumal Gnanakkumaar, Ram Murugesan, Shiek S. S. J. Ahmed
Software Mentions: 1
Published: 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: over 12 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: over 9 years ago

10.1002/path.5335

Overactivity or blockade of transforming growth factor‐β each generate a specific ureter malformation
Cited by: 11
Author(s): Filipa Lopes, Neil Roberts, Leo Zeef, Natalie J. Gardiner, Adrian S. Woolf
Software Mentions: 1
Published: about 5 years ago

10.1002/cjp2.138

High immune cytolytic activity in tumor‐free tongue tissue confers better prognosis in patients with squamous cell carcinoma of the oral tongue
Cited by: 13
Author(s): Xiaolian Gu, Linda Boldrup, Philip J. Coates, Robin Fåhræus, Lixiao Wang, Torben Wilms, Lena Norberg‐Spaak, Nicola Sgaramella, Karin Nylander
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0040538

Temporal Profiling of Gene Networks Associated with the Late Phase of Long-Term Potentiation In Vivo
Cited by: 50
Author(s): Margaret M. Ryan, Brigid Ryan, Madeleine Kyrke-Smith, Barbara Logan, Warren P. Tate, Wickliffe C. Abraham, Joanna M. Williams
Software Mentions: 1
Published: over 12 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962