bioconductor: ArrayExpress | Projects

10.1186/1471-2105-9-183

Data capture in bioinformatics: requirements and experiences with Pedro
Cited by: 16
Author(s): Daniel Jameson, Kevin Garwood, Christopher Garwood, Tim Booth, Pinar Alper, Stephen G. Oliver, Norman W. Paton
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-10-42

Positive correlation between gene coexpression and positional clustering in the zebrafish genome
Cited by: 28
Author(s): Yen Kaow Ng, Wei Wu, Louxin Zhang
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2105-10-S12-S10

Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data
Cited by: 4
Author(s): Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano, Ulrich Pfeffer
Software Mentions: 1
Published: over 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 9 years ago

10.1186/1471-2105-14-8

XperimentR: painless annotation of a biological experiment for the laboratory scientist
Cited by: 7
Author(s): Christopher Tomlinson, Geraint Barton, Mark Woodbridge, Sarah Butcher
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-12-620

An expression map for Anopheles gambiae
Cited by: 27
Author(s): Robert M. MacCallum, Seth Redmond, George K. Christophides
Software Mentions: 1
Published: about 14 years ago

10.3390/ijms21061941

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

10.1186/1471-2164-9-340

Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis
Cited by: 87
Author(s): Marcel Scheideler, Christian Elabd, Laure‐Emmanuelle Zaragosi, Chiara Chiellini, Hubert Hackl, Fátima Sánchez‐Cabo, Sunaina Yadav, Kalina Duszka, Gerald Friedl, Christine Papak, Andreas Prokesch, Reinhard Windhager, Gérard Ailhaud, Christian Dani, Ez-Zoubir Amri, Zlatko Trajanoski
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-6-178

GPX-Macrophage Expression Atlas: A database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults
Cited by: 16
Author(s): Graeme R. Grimes, Stuart Moodie, John S. Beattie, Marie Craigon, Paul Dickinson, Thorsten Forster, Andrew D. Livingston, Muriel Mewissen, Kevin A. Robertson, Alan J. Ross, Garwin K. Sing, Peter Ghazal
Software Mentions: 1
Published: about 20 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: about 11 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: over 6 years ago

10.1186/1471-2164-9-221

Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA
Cited by: 5
Author(s): Matthijs Raaben, Penn Whitley, Diane Bouwmeester, Robert A. Setterquist, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-13-33

Transcriptional ontogeny of the developing liver
Cited by: 41
Author(s): Janice S. Lee, William O. Ward, Geremy W. Knapp, Hongzu Ren, Beena Vallanat, Barbara D. Abbott, Karen J. Ho, Seth J. Karp, J. Christopher Corton
Software Mentions: 1
Published: about 14 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: over 6 years ago

10.1186/1471-2164-11-418

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

10.1186/s12864-019-5464-0

A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes
Cited by: 3
Author(s): Marzena Mura, Roman Jaksik, Anna Lalik, Krzysztof Biernacki, Marek Kimmel, Joanna Rzeszowska-Wolny, Krzysztof Fujarewicz
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2105-8-360

Linking microarray reporters with protein functions
Cited by: 12
Author(s): Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, Chris T. Evelo
Software Mentions: 1
Published: over 18 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 11 years ago

10.1186/1471-2164-7-319

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

10.1186/ar1903

Cited by: 51
Author(s): Johan Lindberg, Erik af Klint, Ann‐Kristin Ulfgren, André Stark, T. Andersson, Peter Nilsson, Lars Klareskog, Joakim Lundeberg
Software Mentions: 1
Published: about 20 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: about 13 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: almost 8 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: over 11 years ago

10.1186/1471-2164-9-3

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

10.1186/1471-2164-8-202

Species differences in brain gene expression profiles associated with adult behavioral maturation in honey bees
Cited by: 48
Author(s): Moushumi Sen Sarma, Charles W. Whitfield, Gene E. Robinson
Software Mentions: 1
Published: about 19 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: almost 7 years ago

10.1186/ar2294

Expression and regulation of CCL18 in synovial fluid neutrophils of patients with rheumatoid arthritis
Cited by: 49
Author(s): Judith Auer, Bläss Markus, Hendrik Schulze‐Koops, Stefan Rußwurm, Thomas Nagel, Joachim R. Kalden, Martin Röllinghoff, H U Beuscher
Software Mentions: 1
Published: about 19 years ago

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 11 years ago

10.3389/fimmu.2013.00353

MicroRNA-Mediated Down-Regulation of M-CSF Receptor Contributes to Maturation of Mouse Monocyte-Derived Dendritic Cells
Cited by: 28
Author(s): Joey Riepsaame, A. Van Oudenaren, Berlinda J. H. den Broeder, Wilfred F. J. van IJcken, Joris Pothof, Pieter J. M. Leenen
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-14-169

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

10.3389/fimmu.2021.653110

Endothelial Immunity Trained by Coronavirus Infections, DAMP Stimulations and Regulated by Anti-Oxidant NRF2 May Contribute to Inflammations, Myelopoiesis, COVID-19 Cytokine Storms and Thromboembolism
Cited by: 37
Author(s): Ying Shao, Jason Saredy, Keman Xu, Yu Sun, Fatma Saaoud, Charles Drummer, Yifan Lu, Jin Jun Luo, Jahaira Lopez-Pastraña, Eric T. Choi, Xiaohua Jiang, Hong Wang, Xiaofeng Yang
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-8-181

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

10.1186/1471-2164-8-387

BMDExpress: a software tool for the benchmark dose analyses of genomic data
Cited by: 160
Author(s): Longlong Yang, Bruce C. Allen, Russell S. Thomas
Software Mentions: 1
Published: over 18 years ago

10.3389/fimmu.2021.631044

An Immunological Perspective: What Happened to Pregnant Women After Recovering From COVID-19?
Cited by: 12
Author(s): Sijia Zhao, Ting Xie, Li Shen, Hong Liu, Liling Wang, Xixiang Ma, Jiankang Wu, Shuiqiao Yuan, Gil Mor, Aihua Liao
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-016-2562-0

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

10.3389/fimmu.2018.01425

Chromatin Binding of c-REL and p65 Is Not Limiting for Macrophage IL12B Transcription During Immediate Suppression by Ovarian Carcinoma Ascites
Cited by: 11
Author(s): Annika Unger, Florian Finkernagel, Nathalie Hoffmann, Felix Neuhaus, Barbara Joos, Andrea Nist, Thorsten Stiewe, Alexander Visekruna, Uwe Wagner, Silke Reinartz, Sabine Müller‐Brüsselbach, Rolf Müller, Till Adhikary
Software Mentions: 1
Published: over 7 years ago

10.3389/fimmu.2016.00272

Transcriptome Analysis of B Cell Immune Functions in Periodontitis: Mucosal Tissue Responses to the Oral Microbiome in Aging
Cited by: 22
Author(s): Jeffrey L. Ebersole, Sreenatha Kirakodu, M. John Novak, Luis Orraca, Janis Gonzalez Martinez, Larry L. Cunningham, Mark V. Thomas, Arnold J. Stromberg, Subramanya Pandruvada, Octavio A. González
Software Mentions: 1
Published: over 9 years ago

10.3389/fimmu.2018.00032

Induction of Short NFATc1/αA Isoform Interferes with Peripheral B Cell Differentiation
Cited by: 4
Author(s): Khalid Muhammad, Ronald Rudolf, Duong Anh Thuy Pham, Stefan Klein-Heßling, Katsuyoshi Takata, Nobuko Matsushita, Volker Ellenrieder, Eisaku Kondo, Edgar Serfling
Software Mentions: 1
Published: about 8 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 6 years ago

10.3389/fimmu.2017.00479

Co-Inflammatory Roles of TGFβ1 in the Presence of TNFα Drive a Pro-inflammatory Fate in Mesenchymal Stem Cells
Cited by: 25
Author(s): Shalom Lerrer, Yulia Liubomirski, Alexander Bott, Khalid Abnaof, Nino Oren, Afsheen Yousaf, Cindy Körner, Tsipi Meshel, Stefan Wiemann, Adit Ben‐Baruch
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-018-4954-9

Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression
Cited by: 13
Author(s): Jochen T. Bick, Veronika L. Flöter, Mark D. Robinson, Stefan Bauersachs, Susanne E. Ulbrich
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-7-113

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

10.1186/2051-5960-2-23

The prognostic role of intragenic copy number breakpoints and identification of novel fusion genes in paediatric high grade glioma
Cited by: 20
Author(s): Diana Carvalho, Alan Mackay, Lynn Bjerke, Richard G. Grundy, Célia Lopes, Rui Manuel Reis, Chris Jones
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-14-301

Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis
Cited by: 53
Author(s): Victoria A Jenkins, Geraint Barton, Brian D. Robertson, Katrina Williams
Software Mentions: 1
Published: almost 13 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: almost 7 years ago

10.3389/fimmu.2020.585414

Oral Microbiome and Gingival Tissue Apoptosis and Autophagy Transcriptomics
Cited by: 10
Author(s): Jeffrey L. Ebersole, Sreenatha Kirakodu, Elliot Neumann, Luis Orraca, Janis Gonzalez Martinez, Octavio A. González
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2020.00438

Dual Pro- and Anti-Inflammatory Features of Monocyte-Derived Dendritic Cells
Cited by: 12
Author(s): Waqas Azeem, Ragnhild Maukon Bakke, Silke Appel, Anne Margrete Øyan, Karl‐Henning Kalland
Software Mentions: 1
Published: almost 6 years ago

10.1186/ar2002

Cited by: 54
Author(s): Betti Giusti, Gabriella Fibbi, Francesca Margheri, Simona Serratì, Luciana Rossi, Filippo Poggi, Ilaria Lapini, Alberto Magi, Angela Del Rosso, Marina Cinelli, Serena Guiducci, Bashar Kahaleh, Laura Bazzichi, Stefano Bombardieri, Marco Matucci‐Cerinic, Gian Franco Gensini, Mario Del Rosso, Rosanna Abbate
Software Mentions: 1
Published: about 20 years ago

10.1186/1471-2164-8-450

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

10.3389/fimmu.2020.00380

Development of a Bioinformatics Framework for Identification and Validation of Genomic Biomarkers and Key Immunopathology Processes and Controllers in Infectious and Non-infectious Severe Inflammatory Response Syndrome
Cited by: 14
Author(s): Dong Tong, Karen E. Kempsell, Tamás Szakmány, Graham Ball
Software Mentions: 1
Published: almost 6 years ago

10.1186/ar2090

Cited by: 71
Author(s): Johan Lindberg, Erik af Klint, Anca I. Catrina, Peter Nilsson, Lars Klareskog, Ann‐Kristin Ulfgren, Joakim Lundeberg
Software Mentions: 1
Published: about 20 years ago

10.1186/1471-2164-14-710

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

10.3389/fmed.2020.527433

Distinct miRNA Gene Expression Profiles Among the Nodule Tissues of Lung Sarcoidosis, Tuberculous Lymphadenitis and Normal Healthy Control Individuals
Cited by: 2
Author(s): Yunan Zhao, Wei Li, Qin Zhang, Yan Yin, Chuanjia Yang, Wen-Xiang Xu, Jian Kang, Ruiqun Qi, Gang Hou
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2019.01157

Inactivation of farR Causes High Rhodomyrtone Resistance and Increased Pathogenicity in Staphylococcus aureus
Cited by: 13
Author(s): Minh Thu Nguyen, Jongkon Saising, Paula María Tribelli, Mulugeta Nega, Seydina M. Diène, Patrice François, Jacques Schrenzel, Cathrin Spröer, Boyke Bunk, Patrick Ebner, Tobias Hertlein, Nimerta Kumari, Thomas Härtner, Dorothee Wistuba, Supayang Piyawan Voravuthikunchai, Ulrike Mäder, Knut Ohlsen, Friedrich Götz
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1000851

Large-Scale Analysis of Network Bistability for Human Cancers
Cited by: 75
Author(s): Tetsuya Shiraishi, Shinako Matsuyama, Hiroaki Kitano
Software Mentions: 1
Published: over 15 years ago

10.3389/fmicb.2017.02039

A Novel TetR-Like Transcriptional Regulator Is Induced in Acid-Nitrosative Stress and Controls Expression of an Efflux Pump in Mycobacteria
Cited by: 9
Author(s): Filomena Perrone, Barbara De Siena, Lidia Muscariello, Sharon L. Kendall, Simon J. Waddell, Margherita Sacco
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1002126

Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach
Cited by: 80
Author(s): Tim D. Williams, Nahid Turan, Amer Diab, Huifeng Wu, Carolynn Mackenzie, Kerry L. Bartie, Olga Hrydziuszko, Brett P. Lyons, Grant D. Stentiford, John Herbert, Kuruvilla Joseph Abraham, Ioanna Katsiadaki, Michael J. Leaver, John B. Taggart, Stephen George, Mark R. Viant, Kevin Chipman, Francesco Falciani
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pcbi.1000940

Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions
Cited by: 63
Author(s): Rong Chen, Tara K. Sigdel, Li Li, Neeraja Kambham, Joel T. Dudley, Szu Chuan Hsieh, R. Bryan Klassen, Amery Chen, Tuyen Caohuu, Alexander A. Morgan, Hannah A. Valantine, Kiran K. Khush, Minnie M. Sarwal, Atul J. Butte
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1003597

Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation
Cited by: 10
Author(s): Marcus J. Tindall, Angela Clerk
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pcbi.1002278

Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
Cited by: 65
Author(s): Dov Greenbaum, Andrea Sboner, Xinmeng Jasmine Mu, Mark Gerstein
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pbio.3001311

MHC class I H2-Kb negatively regulates neural progenitor cell proliferation by inhibiting FGFR signaling
Cited by: 12
Author(s): Karin Lin, Gregor Bieri, Géraldine Gontier, Sören Müller, Lucas K. Smith, Cedric E Snethlage, Charles White, Sun Y. Maybury-Lewis, Saul Villeda
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1004243

The Membrane-Associated Transcription Factor NAC089 Controls ER-Stress-Induced Programmed Cell Death in Plants
Cited by: 160
Author(s): Zhenle Yang, Mei-Jing Wang, Ling Sun, Sun-Jie Lu, Dongling Bi, Li‐Zhong Sun, Ze‐Ting Song, Shuang-Shuang Zhang, Shun-Fan Zhou, Jian‐Xiang Liu
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pbio.0030297

Bioinformatics and Data Management Support for Environmental Genomics
Cited by: 23
Author(s): Dawn Field, Bela Tiwari, Jason Snape
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pgen.1003594

DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts
Cited by: 38
Author(s): Daria V. Zhernakova, Eleonora de Klerk, Harm-Jan Westra, Anastasios Mastrokolias, Shoaib Amini, Yavuz Ariyürek, Ritsert C. Jansen, Brenda W. J. H. Penninx, Jouke Jan Hottenga, Gonneke Willemsen, Eco J. C. de Geus, Dorret I. Boomsma, Jan H. Veldink, Leonard H van den Berg, Cisca Wijmenga, Johan T. den Dunnen, Gert‐Jan B. van Ommen, Peter A C ‘t Hoen, Lude Franke
Software Mentions: 1
Published: over 12 years ago

10.3389/fmicb.2016.00759

The Chromatin of Candida albicans Pericentromeres Bears Features of Both Euchromatin and Heterochromatin
Cited by: 13
Author(s): Verónica Freire-Benéitez, R. Jordan Price, Alessia Buscaino
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pbio.0030384

Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning
Cited by: 394
Author(s): Benoît Guillemette, Alain R. Bataille, Nicolas Gévry, Maryse Adam, Mathieu Blanchette, François Robert, Luc Gaudreau
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pbio.0020317

Submission of Microarray Data to Public Repositories
Cited by: 113
Author(s): Catherine A. Ball, Alvis Brāzma, Helen C. Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, John C. Matese, Helen Parkinson, John Quackenbush, Martin Ringwald, Susanna Assunta Sansone, Gavin Sherlock, Paul T. Spellman, C. J. Stoeckert, Yoshio Tateno, Ron Taylor, Joseph A. White, Neil Winegarden
Software Mentions: 1
Published: over 21 years ago

10.1186/s12864-020-6712-z

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

10.1186/s13007-016-0144-4

Measures for interoperability of phenotypic data: minimum information requirements and formatting
Cited by: 98
Author(s): Hanna Ćwiek‐Kupczyńska, Thomas Altmann, Daniel Arend, Elizabeth Arnaud, Dijun Chen, Guillaume Cornut, Fabio Fiorani, Wojciech Frohmberg, Astrid Junker, Christian Klukas, Matthias Lange, Cezary Mazurek, Anahita Nafissi, Pascal Neveu, Jan van Oeveren, Cyril Pommier, Hendrik Poorter, Philippe Rocca-Serra, Susanna-Assunta Sansone, Uwe Scholz, Marco van Schriek, Ümit Seren, Björn Usadel, Stéphan Weise, Paul J. Kersey, Paweł Krajewski
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1002362

Caenorhabditis elegans Cyclin D/CDK4 and Cyclin E/CDK2 Induce Distinct Cell Cycle Re-Entry Programs in Differentiated Muscle Cells
Cited by: 32
Author(s): Jerome Korzelius, Suzan Ruijtenberg, Martine B.W. Prinsen, Vincent Portegijs, Teije C. Middelkoop, Marian J. A. Groot Koerkamp, Frank C. P. Holstege, Mike Boxem, Sander van den Heuvel
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1000599

A Mouse Model for the Metabolic Effects of the Human Fat Mass and Obesity Associated FTO Gene
Cited by: 290
Author(s): Chris Church, Sheena Lee, Eleanor A. L. Bagg, James S. McTaggart, Robert M. J. Deacon, Thomas A. Gerken, Angela Lee, Lee Moir, Jasmin Mecinović, Mohamed M. Quwailid, Christopher J. Schofield, Frances M. Ashcroft, Roger D. Cox
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pgen.1003160

Insulin and IGF1 Receptors Are Essential for XX and XY Gonadal Differentiation and Adrenal Development in Mice
Cited by: 110
Author(s): Jean-Luc Pitetti, Pierre Calvel, Yannick Romero, Béatrice Conne, Vy Truong, Marilena D. Papaioannou, Olivier Schaad, Mylène Docquier, Pedro Luis Herrera, Dagmar Wilhelm, Serge Nef
Software Mentions: 1
Published: about 13 years ago

10.1111/tpj.14898

TERMINAL FLOWER‐1/CENTRORADIALIS inhibits tuberisation via protein interaction with the tuberigen activation complex
Cited by: 21
Author(s): Xing Zhang, Raymond Campbell, Laurence J. M. Ducreux, Jennifer Morris, Pete E. Hedley, Elena Mellado‐Ortega, Alison G. Roberts, Jennifer Stephens, Glenn Bryan, L. Torrance, Sean Chapman, Salomé Prat, Mark A. Taylor
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1008549

Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs
Cited by: 15
Author(s): Satesh Ramdhani, Elisa Navarro, Evan Udine, Anastasia G. Efthymiou, Brian M Schilder, Madison Parks, Alison M. Goate, Towfique Raj
Software Mentions: 1
Published: about 6 years ago

10.1093/pcp/pcx191

ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index
Cited by: 196
Author(s): Takeshi Obayashi, Yosuke Aoki, Shu Tadaka, Yuki Kagaya, Kengo Kinoshita
Software Mentions: 1
Published: about 8 years ago

10.1093/pcp/pcv165

ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression
Cited by: 143
Author(s): Yosuke Aoki, Yasunobu Okamura, Shu Tadaka, Kengo Kinoshita, Takeshi Obayashi
Software Mentions: 1
Published: over 10 years ago

10.1098/rstb.2010.0286

Computational biology for ageing
Cited by: 37
Author(s): Daniela Wieser, Irene Papatheodorou, Matthias Ziehm, Janet M. Thornton
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pgen.1000846

Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome
Cited by: 220
Author(s): Juan M. Vaquerizas, Ritsuko Suyama, Jop Kind, Kota Miura, Nicholas M. Luscombe, Asifa Akhtar
Software Mentions: 1
Published: almost 16 years ago

10.1098/rstb.2019.0413

Dissecting the interaction of photosynthetic electron transfer with mitochondrial signalling and hypoxic response in the Arabidopsis <i>rcd1</i> mutant
Cited by: 15
Author(s): Alexey Shapiguzov, Lauri Nikkanen, Duncan Fitzpatrick, Julia P. Vainonen, Richard Gossens, Saleh Alseekh, Fayezeh Aarabi, Arjun Tiwari, Olga Blokhina, Klára Panzarová, Zuzana Benedikty, Esa Tyystjärvi, Alisdair R. Fernie, Martin Trtílek, Eva‐Mari Aro, Eevi Rintamäki, Jaakko Kangasjärvi
Software Mentions: 1
Published: almost 6 years ago

10.3390/pharmaceutics11040152

Translational PBPK Modeling of the Protein Therapeutic and CD95L Inhibitor Asunercept to Develop Dose Recommendations for Its First Use in Pediatric Glioblastoma Patients
Cited by: 17
Author(s): Nina Hanke, Claudia Kunz, Meinolf Thiemann, Harald Fricke, Thorsten Lehr
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.10141

Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues
Cited by: 28
Author(s): Sevcan Atay
Software Mentions: 1
Published: over 5 years ago

10.3390/pathogens5030051

FlpS, the FNR-Like Protein of Streptococcus suis Is an Essential, Oxygen-Sensing Activator of the Arginine Deiminase System
Cited by: 10
Author(s): Jörg Willenborg, Anna Koczula, Marcus Fulde, Astrid de Greeff, Andreas Beineke, Wolfgang Eisenreich, Claudia Huber, Maren Seitz, Peter Valentin‐Weigand, Ralph Goethe
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1000479

Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference
Cited by: 117
Author(s): Eric A. Stone, Julien F. Ayroles
Software Mentions: 1
Published: almost 17 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: almost 17 years ago

10.1186/1755-8417-2-2

Unraveling the disease pathogenesis behind lethal hydrolethalus syndrome revealed multiple changes in molecular and cellular level
Cited by: 10
Author(s): Heli Honkala, Jenni Lahtela, Hazel M. Fox, Massimiliano Gentile, Niklas Pakkasjärvi, Riitta Salonen, Kirmo Wartiovaara, Matti Jauhiainen, Marjo Kestilä
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pgen.1003734

Comparative Oncogenomic Analysis of Copy Number Alterations in Human and Zebrafish Tumors Enables Cancer Driver Discovery
Cited by: 31
Author(s): Guangjun Zhang, Sebastian Hoersch, Adam Amsterdam, Charles A. Whittaker, Eline Beert, Julian M. Catchen, Sarah Farrington, John H. Postlethwait, Eric Legius, Nancy Hopkins, Jacqueline A. Lees
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1006000

Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development—Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus
Cited by: 50
Author(s): Katarina Truvé, Peter J. Dickinson, Anqi Xiong, Daniel York, Kartika Jayashankar, Gerli Pielberg, Michele Koltookian, Eva Murén, Hans Henrik Fuxelius, Holger Weishaupt, Fredrik J. Swartling, Gerhard Andersson, Åke Hedhammar, Erik Bongcam‐Rudloff, Karin Forsberg-Nilsson, Danika L. Bannasch, Kerstin Lindblad‐Toh
Software Mentions: 1
Published: almost 10 years ago

10.1186/ar2311

SOX9 transduction of a human chondrocytic cell line identifies novel genes regulated in primary human chondrocytes and in osteoarthritis
Cited by: 61
Author(s): Simon R. Tew, Peter Clegg, Christopher J Brew, C. Redmond, Timothy E. Hardingham
Software Mentions: 1
Published: about 19 years ago

10.3389/fmicb.2018.01952

Coumarin Reduces Virulence and Biofilm Formation in Pseudomonas aeruginosa by Affecting Quorum Sensing, Type III Secretion and C-di-GMP Levels
Cited by: 53
Author(s): Yunhui Zhang, Andrea Saß, Heleen Van Acker, Jasper Wille, Bruno Verhasselt, Filip Van Nieuwerburgh, Volkhard Kaever, Aurélie Crabbé, Tom Coenye
Software Mentions: 1
Published: over 7 years ago

10.1186/ar3062

New insights into the pathogenesis of glucocorticoid-induced avascular necrosis: microarray analysis of gene expression in a rat model
Cited by: 47
Author(s): Mohammad Amin Kerachian, Denis Cournoyer, Edward J. Harvey, Terry Y.-K. Chow, Louis R. Bégin, Ayoub Nahal, Chantal Séguin
Software Mentions: 1
Published: about 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: over 4 years ago

10.1371/journal.pgen.1002398

Widespread Cotranslational Formation of Protein Complexes
Cited by: 104
Author(s): Caia D. S. Duncan, Juan Mata
Software Mentions: 1
Published: about 14 years ago

10.1186/s12957-020-01975-9

Immunohistochemical basigin expression level in thyroid cancer tissues
Cited by: 2
Author(s): Wanping Guo, Deng Tang, Yu‐Yan Pang, Xiao‐Jiao Li, Gang Chen, Zhi‐Guang Huang, Xiao‐Zhun Tang, Quirino Lai, Jin-Yan Gan, Xiaoli Huang, Xiaofan Liu, Zhixiao Wei, Wei Ma
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1005153

A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression
Cited by: 43
Author(s): Marta Garrido, Benjamin Frage, Patrick R. Wright, Anke Becker
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12957-018-1320-y

Clinical value of miR-198-5p in lung squamous cell carcinoma assessed using microarray and RT-qPCR
Cited by: 19
Author(s): Yue‐Ya Liang, Jiacheng Huang, Rongjiang Tang, Wenjie Chen, Peng Chen, Wei‐Luan Cen, Ke Shi, Gao Li, Xiang Gao, An‐Gui Liu, Xuebiao Peng, Su-Hua Huang, Ye‐Ying Fang, Yutong Gu
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.1007256

Broken replication forks trigger heritable DNA breaks in the terminus of a circular chromosome
Cited by: 35
Author(s): Anurag Kumar Sinha, Christophe Possoz, Adeline Durand, Jean-Michel Desfontaines, François‐Xavier Barre, David R. F. Leach, Bertrand Michel
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-017-4200-x

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

10.1007/s10354-016-0488-4

New insights in Rett syndrome using pathway analysis for transcriptomics data
Cited by: 9
Author(s): Friederike Ehrhart, Susan L. Coort, Elisa Cirillo, Eric Smeets, Chris T. Evelo, Leopold Curfs
Software Mentions: 1
Published: over 9 years ago

10.12688/wellcomeopenres.14576.2

DOLORisk: study protocol for a multi-centre observational study to understand the risk factors and determinants of neuropathic pain
Cited by: 20
Author(s): Mathilde M.V. Pascal, Andreas C. Themistocleous, Ralf Baron, Andreas Binder, Didier Bouhassira, Geert Crombez, Nanna Brix Finnerup, Janne Gierthmühlen, Yelena Granovsky, Leif Groop, Harry L. Hébert, Troels Staehelin Jensen, Kristinn Johnsen, Mark I. McCarthy, Meng Wang, Colin N.A. Palmer, Andrew S.C. Rice, Jordi Serra, Romà Solà, David Yarnitsky, Blair H. Smith, Nadine Attal, David L.H. Bennett
Software Mentions: 1
Published: about 7 years ago

10.1186/ar3069

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

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962