bioconductor: ArrayExpress | Projects

10.1186/gb-2014-15-1-r14

Dissecting the expression landscape of RNA-binding proteins in human cancers
Cited by: 195
Author(s): Bobak D. Kechavarzi, Sarath Chandra Janga
Software Mentions: 2
Published: almost 11 years ago

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution
Cited by: 43
Author(s): Dina Raats, Zeev Frenkel, Tamar Krugman, Itay Dodek, Hanan Sela, Hana Šimková, Federica Magni, Federica Cattonaro, Sonia Vautrin, Hélène Bergès, Thomas Wicker, Beat Keller, Philippe Leroy, Romain Philippe, Etienne Paux, Jaroslav Doležel, Catherine Feuillet, Abraham B. Korol, Tzion Fahima
Software Mentions: 2
Published: almost 12 years ago

10.1186/gb-2014-15-4-r62

Arabidopsis replacement histone variant H3.3 occupies promoters of regulated genes
Cited by: 54
Author(s): Huan Shu, Miyuki Nakamura, Alexey Siretskiy, Loris Borghi, Izabel Cristina Freitas Moraes, Thomas Wildhaber, Wilhelm Gruissem, Lars Hennig
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13059-015-0719-9

Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer
Cited by: 42
Author(s): Sehrish Rafique, Jeremy Thomas, Duncan Sproul, Wendy A. Bickmore
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-016-0957-5

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation
Cited by: 62
Author(s): Valentina Proserpio, Andrea Piccolo, Liora Haim-Vilmovsky, Gozde Kar, Tapio Lönnberg, Valentine Svensson, Jhuma Pramanik, Kedar Nath Natarajan, Weichao Zhai, Xiuwei Zhang, Giacomo Donati, Melis Kayikci, Jurij Kotar, Andrew N. J. McKenzie, Ruddy Montandon, Oliver Billker, Steven Woodhouse, Pietro Cicuta, Mario Nicodemi, Sarah A. Teichmann
Software Mentions: 2
Published: over 8 years ago

10.1186/s13059-016-1070-5

Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
Cited by: 1,710
Author(s): Étienne Becht, Nicolás A. Giraldo, Laetitia Lacroix, Bénédicte Buttard, Nabila Elarouci, Florent Petitprez, Janick Sèlves, Pierre Laurent‐Puig, Catheriné Sautès-Fridman, Wolf H. Fridman, Aurélien de Reyniès
Software Mentions: 2
Published: about 8 years ago

10.1186/gb-2004-5-9-r69

Cited by: 199
Author(s): Jingjing Wang, Laura Kean, Jingli Yang, Adrian K. Allan, Shireen A. Davies, Paweł Herzyk, Julian A. T. Dow
Software Mentions: 2
Published: almost 21 years ago

10.1186/s13059-017-1338-4

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses
Cited by: 34
Author(s): Joseph L. Costello, Christopher J. Kershaw, Lydia M. Castelli, David Talavera, William Rowe, Paul F. G. Sims, Mark P. Ashe, Chris M. Grant, Simon J. Hubbard, Graham D. Pavitt
Software Mentions: 2
Published: about 7 years ago

10.1093/gbe/evz103

The Role of Chromatin Accessibility in cis-Regulatory Evolution
Cited by: 14
Author(s): Pei-Chen Peng, Pierre Khoueiry, Charles Girardot, James P. Reddington, David Garfield, Eileen E. M. Furlong, Saurabh Sinha
Software Mentions: 2
Published: over 5 years ago

10.1186/s13073-014-0097-z

Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer’s disease
Cited by: 7
Author(s): Ashutosh Malhotra, Erfan Younesi, Shweta Bagewadi, Martin Hofmann‐Apitius
Software Mentions: 2
Published: almost 10 years ago

10.1136/gutjnl-2017-314817

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
Cited by: 110
Author(s): Judith Kraiczy, Komal Nayak, Kate J. Howell, Alex Ross, Jessica L. Forbester, Camilla Salvestrini, Roxana C. Mustata, Sally Perkins, Amanda Andersson-Rolf, Esther Leenen, Anke Liebert, Ludovic Vallier, Philip Rosenstiel, Oliver Stegle, Gordon Dougan, Robert Heuschkel, Bon–Kyoung Koo, Matthias Zilbauer
Software Mentions: 2
Published: about 7 years ago

10.1016/j.jacbts.2020.09.010

Cardiorenal Tissues Express SARS-CoV-2 Entry Genes and Basigin (BSG/CD147) Increases With Age in Endothelial Cells
Cited by: 30
Author(s): Blerina Ahmetaj‐Shala, Ricky Vaja, Santosh S. Atanur, Peter M. George, Nicholas S. Kirkby, Jane A. Mitchell
Software Mentions: 2
Published: about 4 years ago

10.1172/jci.insight.140785

Neonatal hyperoxia inhibits proliferation and survival of atrial cardiomyocytes by suppressing fatty acid synthesis
Cited by: 15
Author(s): Ethan D. Cohen, Min Yee, George A. Porter, Erin E Ritzer, Andrew McDavid, Paul S. Brookes, Gloria S. Pryhuber, Michael A. O’Reilly
Software Mentions: 2
Published: over 3 years ago

10.1074/jbc.RA118.006865

Translational regulation contributes to the secretory response of chondrocytic cells following exposure to interleukin-1β
Cited by: 10
Author(s): B.T. McDermott, Mandy J. Peffers, Brian McDonagh, Simon R. Tew
Software Mentions: 2
Published: over 5 years ago

10.1186/2041-1480-5-S1-S3

Semantic Web repositories for genomics data using the eXframe platform
Cited by: 7
Author(s): Emily Merrill, Stéphane Corlosquet, Paolo Ciccarese, Tim W. Clark, Sudeshna Das
Software Mentions: 2
Published: almost 11 years ago

10.1186/2041-1480-5-31

CSEO – the Cigarette Smoke Exposure Ontology
Cited by: 8
Author(s): Erfan Younesi, Sam Ansari, Michaela Guendel, Shiva Ahmadi, Chris R. E. Coggins, Julia Hoeng, Martin Hofmann‐Apitius, Manuel C. Peitsch
Software Mentions: 2
Published: over 10 years ago

10.1186/s13326-016-0055-3

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates
Cited by: 7
Author(s): Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson, James Malone
Software Mentions: 2
Published: over 8 years ago

10.1002/stem.2294

Jun-Mediated Changes in Cell Adhesion Contribute to Mouse Embryonic Stem Cell Exit from Ground State Pluripotency
Cited by: 16
Author(s): Giulia Veluscek, Yaoyong Li, Shen-Hsi Yang, Andrew D. Sharrocks
Software Mentions: 2
Published: almost 9 years ago

10.2147/SCCAA.S237361

Informatics Approaches for Harmonized Intelligent Integration of Stem Cell Research
Cited by: 4
Author(s): Joseph Finkelstein, Irena Parvanova, Frederick Zhang
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12976-015-0017-y

PDON: Parkinson’s disease ontology for representation and modeling of the Parkinson’s disease knowledge domain
Cited by: 27
Author(s): Erfan Younesi, Ashutosh Malhotra, Michaela Gündel, Philip Scordis, Alpha Tom Kodamullil, Matt Page, Burkhard Müller, Stephan Springstubbe, Ullrich Wüllner, D. Scheller, Martin Hofmann‐Apitius
Software Mentions: 2
Published: about 9 years ago

10.1128/mBio.00966-18

cAMP Receptor Protein Controls Vibrio cholerae Gene Expression in Response to Host Colonization
Cited by: 41
Author(s): Jainaba Manneh-Roussel, James R. J. Haycocks, Andrés Magán, Nicolás Pérez-Soto, Kerstin Voelz, Andrew Camilli, Anne Marie Krachler, David C. Grainger
Software Mentions: 2
Published: about 6 years ago

10.1128/mBio.00465-20

Chlorpromazine and Amitriptyline Are Substrates and Inhibitors of the AcrB Multidrug Efflux Pump
Cited by: 48
Author(s): Elizabeth Grimsey, Chiara Fais, Robert L. Marshall, Vito Ricci, Maria Laura Ciusa, Jack Stone, Alasdair Ivens, Giuliano Malloci, Paolo Ruggerone, Attilio Vittorio Vargiu, Laura J. V. Piddock
Software Mentions: 2
Published: over 4 years ago

10.1128/mSphere.00579-17

The Small RNA ncS35 Regulates Growth in Burkholderia cenocepacia J2315
Cited by: 15
Author(s): Sanne Kiekens, Andrea Saß, Filip Van Nieuwerburgh, Dieter Deforce, Tom Coenye
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.00014-16

OsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping Regulons
Cited by: 28
Author(s): Mia Urem, Teunke van Rossum, Giselda Bucca, Geri F. Moolenaar, Emma Laing, Magda A. Świątek-Połatyńska, Joost Willemse, Elodie Tenconi, Sébastien Rigali, Nora Goosen, Colin P. Smith, Gilles P. van Wezel
Software Mentions: 2
Published: over 8 years ago

10.1128/mSystems.00186-16

Listeriomics: an Interactive Web Platform for Systems Biology of Listeria
Cited by: 34
Author(s): Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
Software Mentions: 2
Published: over 7 years ago

10.1093/hmg/ddx424

Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort
Cited by: 72
Author(s): Ana Viñuela, Andrew Anand Brown, Alfonso Buil, Pei-Chien Tsai, Matthew N. Davies, Jordana T. Bell, Emmanouil T. Dermitzakis, Timothy D. Spector, Kerrin S. Small
Software Mentions: 2
Published: almost 7 years ago

10.1155/2020/9015713

Classification of Thyroid Nodules with Stacked Denoising Sparse Autoencoder
Cited by: 3
Author(s): Zexin Li, Kaiji Yang, Lili Zhang, Chiju Wei, Peixuan Yang, Weilai Xu
Software Mentions: 2
Published: almost 4 years ago

10.1167/iovs.61.4.24

The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension
Cited by: 13
Author(s): Ilona Liesenborghs, Lars Eijssen, Martina Kutmon, Theo G. M. F. Gorgels, Chris T. Evelo, Henny J. M. Beckers, Carroll A.B. Webers, Jan S.A.G. Schouten
Software Mentions: 2
Published: over 4 years ago

10.1038/onc.2015.526

A RelA(p65) Thr505 phospho-site mutation reveals an important mechanism regulating NF-κB-dependent liver regeneration and cancer
Cited by: 28
Author(s): Anna Moles, Jacqueline Butterworth, Ana M. Sánchez, Jill E. Hunter, Jack Leslie, Hélène Sellier, Dina Tiniakos, Simon Cockell, Derek A. Mann, Fiona Oakley, Neil D. Perkins
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41388-018-0588-2

LCE: an open web portal to explore gene expression and clinical associations in lung cancer
Cited by: 70
Author(s): Ling Cai, Shing-Jong Lin, Luc Girard, Yunyun Zhou, Lin Yang, Bo Ci, Qinbo Zhou, Danni Luo, Bo Yao, Jing Tang, Jeffrey D. Allen, Kenneth E. Huffman, Adi F. Gazdar, John V. Heymach, Ignacio I. Wistuba, Guanghua Xiao, John D. Minna, Yang Xie
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.jmb.2020.10.008

TET1 Interacts Directly with NANOG via Independent Domains Containing Hydrophobic and Aromatic Residues
Cited by: 2
Author(s): Raphaël Pantier, Nicholas P. Mullin, Elisa Hall-Ponselé, Ian Chambers
Software Mentions: 2
Published: about 4 years ago

10.3892/or.2014.3579

Human cancer databases (Review)
Cited by: 63
Author(s): Athanasia Pavlopoulou, Demetrios Α. Spandidos, Ioannis Michalopoulos
Software Mentions: 2
Published: about 10 years ago

10.7554/eLife.44344

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells
Cited by: 102
Author(s): Christopher D. Todd, Özgen Deniz, Darren Taylor, Miguel R. Branco
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.12717

Zeb1 controls neuron differentiation and germinal zone exit by a mesenchymal-epithelial-like transition
Cited by: 58
Author(s): Shalini Singh, Danielle Howell, Niraj Trivedi, Ketty Kessler, Taren Ong, Pedro Rosmaninho, Alexandre A.S.F. Raposo, Giles Robinson, Martine F. Roussel, Diogo S. Castro, David J. Solecki
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.33506

Epidermal LysM receptor ensures robust symbiotic signalling in Lotus japonicus
Cited by: 48
Author(s): Eiichi Murakami, Jeryl Cheng, Kira Gysel, Zoltán Bozsóki, Yasuyuki Kawaharada, Christian T. Hjuler, Kasper K. Sørensen, Ke Tao, Simon Kelly, Francesco Venice, Andrea Genre, Mikkel B. Thygesen, Noor de Jong, Maria Vinther, Dorthe Bødker Jensen, Knud J. Jensen, Mickaël Blaise, Lene Heegaard Madsen, Kasper R. Andersen, Jens Stougaard, Simona Radutoiu
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.65722

Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast
Cited by: 18
Author(s): Rong Yu, Egor Vorontsov, Carina Sihlbom, Jens Nielsen
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.18715

A computational interactome and functional annotation for the human proteome
Cited by: 59
Author(s): José Ignacio Garzón, Lei Deng, Diana Murray, Sagi Shapira, Donald Petrey, Barry Honig
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.33761

Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair
Cited by: 116
Author(s): Nataša Savić, Femke Ringnalda, Helen Lindsay, Christian Berk, Katja Bargsten, Yizhou Li, Dario Neri, Mark D. Robinson, Constance Ciaudo, Jonathan Hall, Martin Jínek, Gerald Schwank
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms141123160

Systems Biology Approach to the Dissection of the Complexity of Regulatory Networks in the S. scrofa Cardiocirculatory System
Cited by: 4
Author(s): Paolo Martini, Gabriele Sales, Enrica Calura, Mattia Brugiolo, Gerolamo Lanfranchi, Chiara Romualdi, Stefano Cagnin
Software Mentions: 2
Published: about 11 years ago

10.3390/ijms151017601

Hope for GWAS: Relevant Risk Genes Uncovered from GWAS Statistical Noise
Cited by: 2
Author(s): Catarina Correia, Yoan Diekmann, Astrid M. Vicente, José B. Pereira-Leal
Software Mentions: 2
Published: about 10 years ago

10.3390/ijms161226148

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders
Cited by: 41
Author(s): Martin Hofmann-Apitius, G. Ball, Stephan Gebel, Shweta Bagewadi, Bernard de Bono, Reinhard Schneider, Matt Page, Alpha Tom Kodamullil, Erfan Younesi, Christian Ebeling, Jesper Tegnér, Luc Canard
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms20194740

The CXCR4–CXCL12-Axis Is of Prognostic Relevance in DLBCL and Its Antagonists Exert Pro-Apoptotic Effects In Vitro
Cited by: 13
Author(s): Katrin Pansy, Julia Feichtinger, Barbara Ehall, Barbara Uhl, Miriam Sedej, David Roula, Beata Pursche, Axel Wolf, Manuel Zoidl, Elisabeth Steinbauer, Verena Gruber, Hildegard Greinix, Katharina Prochazka, Gerhard G. Thallinger, Ákos Heinemann, Christine Beham–Schmid, Peter Neumeister, Tanja Wrodnigg, Karoline Fechter, Alexander Deutsch
Software Mentions: 2
Published: about 5 years ago

10.3390/cells10030674

Acyl–Acyl Carrier Protein Desaturases and Plant Biotic Interactions
Cited by: 11
Author(s): Sami Kazaz, Romane Miray, Sébastien Baud
Software Mentions: 1
Published: over 3 years ago

10.3390/cells8121554

Transcriptional Characterization of Stage I Epithelial Ovarian Cancer: A Multicentric Study
Cited by: 9
Author(s): Enrica Calura, Matteo Ciciani, Andrea Sambugaro, Lara Paracchini, Giuseppe Benvenuto, Salvatore Milite, Paolo Martini, Luca Beltrame, Flaminia Zane, Robert Fruscio, Martina Delle Marchette, Fulvio Borella, Germana Tognon, Antonella Ravaggi, Dionyssios Katsaros, Eliana Bignotti, Franco Odicino, Maurizio D’Incalci, Sergio Marchini, Chiara Romualdi
Software Mentions: 1
Published: almost 5 years ago

10.3390/cells9010142

Dissecting Mechanisms of Melanoma Resistance to BRAF and MEK Inhibitors Revealed Genetic and Non-Genetic Patient- and Drug-Specific Alterations and Remarkable Phenotypic Plasticity
Cited by: 41
Author(s): Mariusz L. Hartman, Małgorzata Sztiller-Sikorska, Anna Gajos-Michniewicz, Małgorzata Czyż
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41436-018-0015-7

A homozygous FANCM frameshift pathogenic variant causes male infertility
Cited by: 61
Author(s): Hong Yin, Hui Ma, Sajjad Hussain, Huan Zhang, Xuefeng Xie, Long Jiang, Xiaohua Jiang, Furhan Iqbal, Ihtisham Bukhari, Hanwei Jiang, Asim Ali, Liangwen Zhong, Tao Li, Suixing Fan, Beibei Zhang, Jianing Gao, Yang Li, Nazish Jabeen, Teka Khan, Manan Khan, Muhammad Zubair, Qiaomei Hao, Hui Fang, Jun Huang, Mahmoud Huleihel, Jiahao Sha, Tej K. Pandita, Yuanwei Zhang, Qinghua Shi
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12711-020-00587-x

Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)
Cited by: 8
Author(s): Hanne Dvergedal, Thomas Nelson Harvey, Yang Jin, Jørgen Ødegård, Lars Grønvold, Simen Rød Sandve, Dag Inge Våge, Thomas Moen, G. Klemetsdal
Software Mentions: 1
Published: about 4 years ago

10.1534/genetics.116.197376

Identification of Ceruloplasmin as a Gene that Affects Susceptibility to Glomerulonephritis Through Macrophage Function
Cited by: 11
Author(s): Tai‐Di Chen, Maxime Rotival, Ling-Yin Chiu, Marta Bagnati, Jeong‐Hun Ko, Prashant K. Srivastava, Enrico Petretto, Charles D. Pusey, Ping-Chin Lai, Timothy J. Aitman, H. Terence Cook, Jacques Behmoaras
Software Mentions: 1
Published: over 7 years ago

10.1534/genetics.119.302493

Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Heliconius Butterflies
Cited by: 28
Author(s): Ana Catalán, Adriana D. Briscoe, Sebastian Höhna
Software Mentions: 1
Published: about 5 years ago

10.1016/j.gdata.2014.10.016

Transcriptional ontogeny of first trimester human fetal and placental mesenchymal stem cells: Gestational age versus niche
Cited by: 5
Author(s): Jennifer Ryan, Nicholas Matigian, Rebecca A. Pelekanos, Samuel Jesuadian, Christine A. Wells, Nicholas M. Fisk
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0063184

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

10.1186/gb-2005-6-11-r94

Cited by: 155
Author(s): Bregje Wertheim, Alex R. Kraaijeveld, Eugene F. Schuster, Eric Blanc, Meirion Hopkins, Scott D. Pletcher, Michael R. Strand, Linda Partridge, H. C. J. Godfray
Software Mentions: 1
Published: almost 20 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

10.1186/gb-2005-6-7-r56

Cited by: 41
Author(s): Shiri Freilich, Tim Massingham, Sumit Bhattacharyya, Hannes Ponstingl, Paul Lyons, Tom C. Freeman, Janet M. Thornton
Software Mentions: 1
Published: almost 20 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

10.1186/gb-2006-7-3-r26

Cited by: 40
Author(s): Colin C. Pritchard, David A. Coil, Sarah Hawley, Li Hsu, Peter S. Nelson
Software Mentions: 1
Published: almost 19 years ago

10.1186/gb-2006-7-6-r46

Cited by: 39
Author(s): Emma Laing, Vassilis Mersinias, Colin P. Smith, Simon J. Hubbard
Software Mentions: 1
Published: almost 19 years ago

10.1186/gb-2006-7-12-r114

Cited by: 56
Author(s): Hanni Willenbrock, Carsten Friis, Agnieszka Sierakowska Juncker, David W. Ussery
Software Mentions: 1
Published: almost 19 years ago

10.1186/gb-2006-7-9-r84

Cited by: 140
Author(s): Katleen De Preter, Jo Vandesompele, Pierre Heimann, Nurten Yigit, Siv Beckman, Alexander Schramm, Angelika Eggert, Raymond L. Stallings, Yves Benoît, Marleen Renard, Anne De Paepe, Geneviève Laureys, Sven Påhlman, Franki Speleman
Software Mentions: 1
Published: almost 19 years ago

10.1186/gb-2006-7-10-r99

Cited by: 78
Author(s): Anders F. Andersson, Magnus Lundgren, Stefan Eriksson, Magnus Rosenlund, Rolf Bernander, Peter Nilsson
Software Mentions: 1
Published: almost 19 years ago

10.1186/gb-2006-7-10-r89

Cited by: 25
Author(s): Shiri Freilich, Tim Massingham, Eric Blanc, Leon Goldovsky, Janet M. Thornton
Software Mentions: 1
Published: almost 19 years ago

10.1186/gb-2006-7-11-r107

Cited by: 211
Author(s): Birgitte Regenberg, Thomas Grotkjær, Ole Winther, Anders Fausbøll, Mats Åkesson, Christoffer Bro, Lars Kai Hansen, Søren Brunak, Jens Nielsen
Software Mentions: 1
Published: almost 19 years ago

10.1186/gb-2007-8-5-r74

Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies
Cited by: 23
Author(s): Björn Nilsson, Petra Håkansson, Mikael Johansson, Sven Nelander, Thoas Fioretos
Software Mentions: 1
Published: almost 18 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 18 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 12 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: about 10 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 5 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 18 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 17 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 18 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 18 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 17 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 17 years ago

10.1371/journal.pone.0141710

Expression of CCL20 and Its Corresponding Receptor CCR6 Is Enhanced in Active Inflammatory Bowel Disease, and TLR3 Mediates CCL20 Expression in Colonic Epithelial Cells
Cited by: 51
Author(s): Helene Kolstad Skovdahl, Atle van Beelen Granlund, Ann Elisabet Østvik, Ingrid Bakke, Sverre Helge Torp, Jan Kristian Damås, Arne K. Sandvik
Software Mentions: 1
Published: about 9 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 16 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

10.3390/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: about 5 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 16 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

10.1371/journal.pgen.1000470

SWI/SNF Associates with Nascent Pre-mRNPs and Regulates Alternative Pre-mRNA Processing
Cited by: 75
Author(s): Anu Tyagi, Jessica Ryme, David Brodin, A K Ostlund Farrants, Neus Visa
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 5 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 16 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 13 years ago

10.1371/journal.pone.0215452

Array expression meta-analysis of cancer stem cell genes identifies upregulation of PODXL especially in DCC low expression meningiomas
Cited by: 4
Author(s): Hans-Juergen Schulten, Deema Hussein
Software Mentions: 1
Published: over 5 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 14 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 14 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

10.1371/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

10.1371/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

10.1371/journal.pone.0043249

Induction of Endoplasmic Reticulum Stress Response by the Indole-3-Carbinol Cyclic Tetrameric Derivative CTet in Human Breast Cancer Cell Lines
Cited by: 43
Author(s): Luca Galluzzi, Mauro De Santi, Rita Crinelli, Cinzia De Marco, Nadia Zaffaroni, Andrea Duranti, Giorgio Brandi, Mauro Magnani
Software Mentions: 1
Published: 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 12 years ago

10.1371/journal.pone.0052321

Focal DNA Copy Number Changes in Neuroblastoma Target MYCN Regulated Genes
Cited by: 37
Author(s): Candy Kumps, Annelies Fieuw, Pieter Mestdagh, Björn Menten, Steve Lefever, Filip Pattyn, Sara De Brouwer, Tom Sante, Johannes H. Schulte, Alexander Schramm, Nadine Van Roy, Tom Van Maerken, Rosa Noguera, Valérie Combaret, Christine Devalck, Frank Westermann, Geneviève Laureys, Angelika Eggert, Jo Vandesompele, Katleen De Preter, Franki Speleman
Software Mentions: 1
Published: almost 12 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.pntd.0002438

Temephos Resistance in Aedes aegypti in Colombia Compromises Dengue Vector Control
Cited by: 106
Author(s): Nelson Grisales, Rodolphe Poupardin, Santiago Gómez, Idalyd Fonseca-González, Hilary Ranson, Audrey Lenhart
Software Mentions: 1
Published: about 11 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

10.1186/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 10 years ago

10.1371/journal.pone.0023466

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

10.1371/journal.pntd.0002607

Bioassay-Guided Fractionation of Extracts from Codiaeum variegatum against Entamoeba histolytica Discovers Compounds That Modify Expression of Ceramide Biosynthesis Related Genes
Cited by: 14
Author(s): Emmanuel Mfotie Njoya, Christian Weber, Nora Adriana Hernández‐Cuevas, Chung-Chau Hon, Yves L. Janin, Melanie F. G. Kamini, Paul Fewou Moundipa, Nancy Guillén
Software Mentions: 1
Published: almost 11 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 11 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 11 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962