bioconductor: ArrayExpress | Projects

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: almost 6 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 5 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: about 7 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 13 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 12 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 10 years ago

10.1111/jcmm.15429

Bioinformatics analysis of the biological changes involved in the osteogenic differentiation of human mesenchymal stem cells
Cited by: 16
Author(s): Tao Fan, Rongmei Qu, Qinghe Yu, Bing Sun, Xin Jiang, Yuchao Yang, Xiaolan Huang, Zhaoxi Zhou, Jun Ouyang, Shizhen Zhang, Jingxing Dai
Software Mentions: 2
Published: over 6 years ago

10.1242/jcs.226969

An essential role for dNTP homeostasis following CDK-induced replication stress
Cited by: 15
Author(s): Chen Chun Pai, Kuo–Feng Hsu, Samuel C. Durley, Andrea Keszthelyi, Stephen Kearsey, Charalampos Rallis, Lisa K. Folkes, Rachel S. Deegan, Sarah E. Wilkins, Sophia X. Pfister, Nagore de León, Christopher J. Schofield, Jürg Bähler, Antony Carr, Timothy C. Humphrey
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.0010045

Bordetella pertussis, the Causative Agent of Whooping Cough, Evolved from a Distinct, Human-Associated Lineage of B. bronchiseptica
Cited by: 238
Author(s): Dimitri A. Diavatopoulos, Craig Cummings, Leo M. Schouls, Mary M. Brinig, David A. Relman, Frits R. Mooi
Software Mentions: 2
Published: almost 21 years ago

10.1371/journal.ppat.1000105

Anti-Fungal Innate Immunity in C. elegans Is Enhanced by Evolutionary Diversification of Antimicrobial Peptides
Cited by: 215
Author(s): Nathalie Pujol, Olivier Zugasti, Daniel Wong, Carole Couillault, C. Léopold Kurz, Hinrich Schulenburg, Jonathan J. Ewbank
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.ppat.1002027

Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival
Cited by: 133
Author(s): Hebert Echenique-Rivera, Alessandro Muzzi, Elena Del Tordello, Kate L. Seib, Patrice François, Rino Rappuoli, Mariagrazia Pizza, Davide Serruto
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.ppat.1002046

Transition of Plasmodium Sporozoites into Liver Stage-Like Forms Is Regulated by the RNA Binding Protein Pumilio
Cited by: 88
Author(s): Carina S. S. Gomes-Santos, Joanna A. M. Braks, Miguel Prudêncio, Céline Carret, Ana Gomes, Arnab Pain, Theresa Feltwell, Shahid M. Khan, Andrew P. Waters, Chris J. Janse, Gunnar R. Mair, Maria M. Mota
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.ppat.1004609

Promiscuous RNA Binding Ensures Effective Encapsidation of APOBEC3 Proteins by HIV-1
Cited by: 77
Author(s): Luis Apolonia, Reiner Schulz, Tomaž Curk, Paula Rocha, Chad M. Swanson, Torsten Schaller, Jernej Ule, Michael H. Malim
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.ppat.1007729

Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution
Cited by: 16
Author(s): Audrey M. V. Ah‐Fong, Meenakshi S. Kagda, Melania Abrahamian, Howard S. Judelson
Software Mentions: 2
Published: over 7 years ago

10.1098/rsos.150402

Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts
Cited by: 21
Author(s): Brett Trost, Catherine A. Moir, Zoe E. Gillespie, Anthony Kusalik, Jennifer A. Mitchell, Christopher H. Eskiw
Software Mentions: 2
Published: about 11 years ago

10.1016/j.redox.2020.101450

Mitochondrial complex I derived ROS regulate stress adaptation in Drosophila melanogaster
Cited by: 37
Author(s): Filippo Scialò, Ashwin Sriram, Rhoda Stefanatos, Ruth V. Spriggs, Samantha H. Y. Loh, L. Miguel Martins, Alberto Sanz
Software Mentions: 2
Published: over 6 years ago

10.1186/1477-7827-7-94

A cross-study gene set enrichment analysis identifies critical pathways in endometriosis
Cited by: 20
Author(s): Hang Zhao, Qishan Wang, Chen Bai, Kan He, Yuchun Pan
Software Mentions: 2
Published: about 17 years ago

10.1186/s12958-015-0088-y

The rat placental renin-angiotensin system - a gestational gene expression study
Cited by: 14
Author(s): Kanchan Vaswani, Hsiu‐Wen Chan, Pali Verma, Marloes Dekker Nitert, Hassendrini N. Peiris, Ryan J Wood-Bradley, James A. Armitage, Gregory E. Rice, Murray D. Mitchell
Software Mentions: 2
Published: about 11 years ago

10.1093/rheumatology/kez358

Interleukin-36 family dysregulation drives joint inflammation and therapy response in psoriatic arthritis
Cited by: 29
Author(s): Marie-Astrid Boutet, Alessandra Nerviani, Gloria Lliso-Ribera, Davide Lucchesi, Edoardo Prediletto, Giulia Maria Ghirardi, Katriona Goldmann, Myles Lewis, Costantino Pitzalis
Software Mentions: 2
Published: about 7 years ago

10.1186/1939-8433-5-17

The Rice Oligonucleotide Array Database: an atlas of rice gene expression
Cited by: 156
Author(s): Peijian Cao, Ki‐Hong Jung, Daeseok Choi, Daehee Hwang, Jun Zhu, Pamela C. Ronald
Software Mentions: 2
Published: about 14 years ago

10.1038/sdata.2014.11

Genomes and phenomes of a population of outbred rats and its progenitors
Cited by: 28
Author(s): Amelie Baud, Victor Guryev, Oliver Hummel, Martina Johannesson, Amelie Baud, Victor Guryev, Oliver Hummel, Martina Johannesson, Roel Hermsen, Pernilla Stridh, Delyth Graham, Martin W. McBride, Tatiana Foroud, Sophie Caldérari, Margarita Diez, Johan Öckinger, Amennai Daniel Beyeen, Alan Gillett, Nada Abdelmagid, André Ortlieb Guerreiro-Cacais, Maja Jagodic, Jonatan Tuncel, Ulrika Norin, Elisabeth Beattie, Ngan Huynh, William H. Miller, Daniel L. Koller, Imranul Alam, Samreen Falak, Mary Osborne-Pellegrin, Esther Martínez-Membrives, Toni Cañete, Gloria Blázquez, Elia Vicens-Costa, Carme Mont-Cardona, Sira Díaz-Morán, Adolf Tobeña, Diana Zélénika, Kathrin Saar, Giannino Patone, Anja Bauerfeind, Marie-Thérèse Bihoreau, Matthias Heinig, Youngae Lee, Carola Rintisch, Herbert Schulz, David A. Wheeler, Kim C. Worley, Donna M. Muzny, Richard A. Gibbs, Mark Lathrop, Nico Lansu, Pim W. Toonen, Frans Paul Ruzius, Ewart de Bruijn, Heidi Hauser, David J. Adams, Thomas Keane, Santosh S. Atanur, Tim Aitman, Paul Flicek, Tomas Malinauskas, Elizabeth Jones, Diana Ekman, Regina López-Aumatell, Anna F. Dominiczak, Rikard Holmdahl, Tomas Olsson, Dominique Guyader, Norbert Hübner, Alberto Fernández-Teruel, Edwin Cuppen, Richard Mott, Jonathan Flint, Jonathan Flint
Software Mentions: 2
Published: over 12 years ago

10.1038/sdata.2018.13

Single cell RNA sequencing of stem cell-derived retinal ganglion cells
Cited by: 41
Author(s): Maciej Daniszewski, Anne Senabouth, Quan Nguyen, Duncan E. Crombie, Samuel W. Lukowski, Tejal Kulkarni, Valentin M. Sluch, Jafar S. Jabbari, Xitiz Chamling, Donald J. Zack, Alice Pébay, Joseph E. Powell, Alex W. Hewitt
Software Mentions: 2
Published: over 8 years ago

10.1038/sdata.2018.158

The REMBRANDT study, a large collection of genomic data from brain cancer patients
Cited by: 101
Author(s): Yuriy Gusev, Krithika Bhuvaneshwar, Lei Song, Jean-Claude Zenklusen, Howard A. Fine, Subha Madhavan
Software Mentions: 2
Published: about 8 years ago

10.1038/s41597-020-00636-6

Cross-sectional study of human coding- and non-coding RNAs in progressive stages of Helicobacter pylori infection
Cited by: 1
Author(s): Sergio Lario, María José Ramírez‐Lázaro, Aintzane González-Lahera, José L. Lavín, María Vila-Casadesús, María Elisa Quílez, Anna Brunet-Vega, Juan José Lozano, Ana M. Aransay, Xavier Calvet
Software Mentions: 2
Published: about 6 years ago

10.1038/s41597-021-00808-y

Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials
Cited by: 17
Author(s): Laura Aliisa Saarimäki, Antonio Federico, Iseult Lynch, Anastasios G. Papadiamantis, Andreas Tsoumanis, Georgia Melagraki, Antreas Afantitis, Angela Serra, Dario Greco
Software Mentions: 2
Published: over 5 years ago

10.1038/srep13113

Human cell dedifferentiation in mesenchymal condensates through controlled autophagy
Cited by: 34
Author(s): Rebecca Rose Pennock, Elen Bray, Paul R. Pryor, Sally James, Paul J. McKeegan, Roger G. Sturmey, Paul G. Genever
Software Mentions: 2
Published: about 11 years ago

10.1038/srep17470

Fine-tuned SRF activity controls asymmetrical neuronal outgrowth: implications for cortical migration, neural tissue lamination and circuit assembly
Cited by: 14
Author(s): Marilyn Scandaglia, Eva Benito, Cruz Morenilla‐Palao, Anna Fiorenza, Beatriz del Blanco, Yaiza Coca, Eloı́sa Herrera, Ángel Barco
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep19729

Nucleosome architecture throughout the cell cycle
Cited by: 27
Author(s): Özgen Deniz, Oscar Flores, Martí Aldea, Montserrat Soler-López, Modesto Orozco
Software Mentions: 2
Published: over 10 years ago

10.1038/srep31209

Dysregulated immune system networks in war veterans with PTSD is an outcome of altered miRNA expression and DNA methylation
Cited by: 69
Author(s): Marpe Bam, Xiaoming Yang, Elizabeth E. Zumbrun, Zhimin Yin, Juhua Zhou, J. P. Ginsberg, Quinne Leyden, Jiajia Zhang, Prakash Nagarkatti, Mitzi Nagarkatti
Software Mentions: 2
Published: about 10 years ago

10.1038/srep37988

Global gene regulation during activation of immunoglobulin class switching in human B cells
Cited by: 22
Author(s): Youming Zhang, David Fear, Saffron A.G. Willis‐Owen, William Cookson, Miriam F. Moffatt
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-017-01141-4

The yeast osmostress response is carbon source dependent
Cited by: 52
Author(s): Roja Babazadeh, Petri‐Jaan Lahtvee, Caroline B. Adiels, Mattias Goksör, Jens Nielsen, Stefan Hohmann
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-03986-1

Prediction of lncRNA-protein interactions using HeteSim scores based on heterogeneous networks
Cited by: 70
Author(s): Yun Xiao, Jingpu Zhang, Lei Deng
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-05451-5

Loss of Usp9x disrupts cell adhesion, and components of the Wnt and Notch signaling pathways in neural progenitors
Cited by: 26
Author(s): Susitha Premarathne, Mariyam Murtaza, Nicholas Matigian, Lachlan A. Jolly, Stephen A. Wood
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-09430-8

Cerium oxide nanoparticles inhibit differentiation of neural stem cells
Cited by: 59
Author(s): Anda R. Gliga, Karin Edoff, Fanny Caputo, Thomas Källman, Hans Blom, Hanna Karlsson, Lina Ghibelli, Enrico Traversa, Sandra Ceccatelli, Bengt Fadeel
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-18043-0

Aedes aegypti microRNA miR-2b regulates ubiquitin-related modifier to control chikungunya virus replication
Cited by: 21
Author(s): Sunil Kumar Dubey, Jatin Shrinet, Jaspreet Jain, Shakir Ali, Sujatha Sunil
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-018-19357-3

TPGLDA: Novel prediction of associations between lncRNAs and diseases via lncRNA-disease-gene tripartite graph
Cited by: 73
Author(s): Liang Ding, Minghui Wang, Dongdong Sun, Ao Li
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-019-44235-x

Cynomolgus macaque IL37 polymorphism and control of SIV infection
Cited by: 3
Author(s): Takashi Shiina, Shingo Suzuki, Nicolas Congy-Jolivet, Alice Aarnink, Henri‐Jean Garchon, Nathalie Dereuddre‐Bosquet, Bruno Vaslin, Nicolas Tchitchek, Delphine Desjardins, Brigitte Autran, Olivier Lambotte, Ioannis Théodorou, Roger Le Grand, Antoine Blancher
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-57076-5

The ETS transcription factor ETV5 is a target of activated ALK in neuroblastoma contributing to increased tumour aggressiveness
Cited by: 19
Author(s): Liselot Mus, Irina Lambertz, Shana Claeys, Candy Kumps, Wouter Van Loocke, Christophe Van Neste, Ganesh Umapathy, Marica Vaapil, Christoph Bartenhagen, Geneviève Laureys, Olivier De Wever, Daniel Bexell, Matthias Fischer, Bengt Hållberg, Johannes H. Schulte, Bram De Wilde, Kaat Durinck, Geertrui Denecker, Katleen De Preter, Frank Speleman
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-59514-1

Combined HER3-EGFR score in triple-negative breast cancer provides prognostic and predictive significance superior to individual biomarkers
Cited by: 24
Author(s): Angela Ogden, Shristi Bhattarai, Bikram Sahoo, Nigel P. Mongan, Mansour Alsaleem, Andrew Green, Mohammed A. Aleskandarany, Ian O. Ellis, Sonal Pattni, Xiaoxian Bill Li, Carlos S. Moreno, Uma Krishnamurti, Emiel A. M. Janssen, Kristín Jónsdóttir, Emad A. Rakha, Padmashree C.G. Rida, Ritu Aneja
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-60235-8

Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction
Cited by: 8
Author(s): Jessica Gliozzo, Paolo Perlasca, Marco Mesiti, Elena Casiraghi, Viviana Vallacchi, Elisabetta Vergani, Giuliano Grossi, Alessandro Petrini, Matteo Ré, Alberto Paccanaro, Giorgio Valentini
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-74417-x

Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)
Cited by: 9
Author(s): Ying Li, Qilu Song, Yamin Zhang, Zheng Li, Jialin Guo, Xinhong Chen, Gaisheng Zhang
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-74288-2

Cell-free DNA in plasma as an essential immune system regulator
Cited by: 19
Author(s): Marie Korabečná, Alžběta Zinková, Iva Brynychova, Blanka Chylíková, Petr Přikryl, Lucie Šedová, Pavel Neužil, Ondřej Šeda
Software Mentions: 2
Published: about 6 years ago

10.1186/1752-0509-4-86

Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems
Cited by: 7
Author(s): Michał Dąbrowski, Norbert Dojer, Małgorzata Zawadzka, Jakub Mieczkowski, Bożena Kamińska
Software Mentions: 1
Published: over 16 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: about 19 years ago

10.1371/journal.pone.0048363

Functional Similarities between Pigeon ‘Milk’ and Mammalian Milk: Induction of Immune Gene Expression and Modification of the Microbiota
Cited by: 28
Author(s): Meagan J Gillespie, Dragana Stanley, Honglei Chen, John A. Donald, Kevin R. Nicholas, Robert J. Moore, Tamsyn M. Crowley
Software Mentions: 1
Published: almost 14 years ago

10.1186/1752-0509-3-86

Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network
Cited by: 39
Author(s): Osnat Atias, Benny Chor, Daniel Chamovitz
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0080747

PaGenBase: A Pattern Gene Database for the Global and Dynamic Understanding of Gene Function
Cited by: 100
Author(s): Jianbo Pan, Shichang Hu, Dan Shi, Mei-Chun Cai, Yin-Bo Li, Quan Zou, Zhi-Liang Ji
Software Mentions: 1
Published: almost 13 years ago

10.1186/1752-0509-9-S2-S3

KPP: KEGG Pathway Painter
Cited by: 18
Author(s): Ganiraju C. Manyam, Aybike Birerdinc, Ancha Baranova
Software Mentions: 1
Published: over 11 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: almost 21 years ago

10.1371/journal.pone.0026023

Hormone Receptor and ERBB2 Status in Gene Expression Profiles of Human Breast Tumor Samples
Cited by: 6
Author(s): Anna Dvorkin‐Gheva, John A. Hassell
Software Mentions: 1
Published: about 15 years ago

10.1186/2041-1480-5-37

CLO: The cell line ontology
Cited by: 84
Author(s): Sirarat Sarntivijai, Yuling Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew Brush, Melissa Haendel, Jie Zheng, Christian J. Stoeckert, Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0250747

Glycans unique to the relapse-prone subset within triple-negative breast cancer as revealed by lectin array-based analysis of surgical specimens
Cited by: 3
Author(s): Madoka Sakata-Matsuzawa, Kaori Denda-Nagai, Haruhiko Fujihira, Miki Noji, Katrin Ishii-Schrade, Atsushi Matsuda, Atsushi Kuno, Misato Okazaki, Keiichi Nakai, Yoshiya Horimoto, Mitsue Saito, Tatsuro Irimura
Software Mentions: 1
Published: over 5 years ago

10.1186/1752-0509-5-68

Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus
Cited by: 37
Author(s): Ian M. Overton, Shirley A. Graham, Katherine A. Gould, Jason Hinds, Catherine H. Botting, Sally L. Shirran, Geoffrey J. Barton, Peter J. Coote
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12918-018-0579-5

New perspectives: systems medicine in cardiovascular disease
Cited by: 13
Author(s): Frank Krämer, Steffen Just, Tanja Zeller
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0113053

Toward Computational Cumulative Biology by Combining Models of Biological Datasets
Cited by: 8
Author(s): Ali Faisal, Jaakko Peltonen, Elisabeth Georgii, Johan Rung, Samuel Kaski
Software Mentions: 1
Published: almost 12 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: almost 20 years ago

10.1371/journal.pone.0080047

A Small RNA Encoded in the Rv2660c Locus of Mycobacterium tuberculosis Is Induced during Starvation and Infection
Cited by: 32
Author(s): Joanna Houghton, Teresa Cortes, Olga T. Schubert, Graham Rose, Angela Rodgers, Megan De Ste Croix, Rudolf Aebersold, Douglas B. Young, Kristine B. Arnvig
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0139446

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions
Cited by: 32
Author(s): Francesco Iorio, Roshan L. Shrestha, Nicolas Levin, Viviane Boilot, Mathew J. Garnett, Julio Sáez-Rodríguez, Viji M. Draviam
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0001403

Probing Host Pathogen Cross-Talk by Transcriptional Profiling of Both Mycobacterium tuberculosis and Infected Human Dendritic Cells and Macrophages
Cited by: 185
Author(s): Ludovic Tailleux, Simon J. Waddell, Mattia Pelizzola, Alessandra Mortellaro, Michael Withers, Antoine Tanne, Paola Ricciardi Castagnoli, Brigitte Gicquel, Neil G. Stoker, Philip D. Butcher, Maria Foti, Olivier Neyrolles
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2105-9-379

MiMiR – an integrated platform for microarray data sharing, mining and analysis
Cited by: 18
Author(s): Christopher Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L. Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Timothy J. Aitman, Laurence Gamé
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0082684

Genetic Interaction between Mutations in c-Myb and the KIX Domains of CBP and p300 Affects Multiple Blood Cell Lineages and Influences Both Gene Activation and Repression
Cited by: 27
Author(s): Lawryn H. Kasper, Tsutomu Fükuyama, Stephanie Lerach, Yunchao Chang, Wu Xu, Song Wu, Kelli L. Boyd, Paul K. Brindle
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0106278

SDF-1 Chemokine Signalling Modulates the Apoptotic Responses to Iron Deprivation of Clathrin-Depleted DT40 Cells
Cited by: 2
Author(s): Alena Pance, Frank Ralf Morrissey-Wettey, Helen Craig, Alison Downing, Richard Talbot, Antony P. Jackson
Software Mentions: 1
Published: about 12 years ago

10.7150/jca.29293

Clinical Significance of microRNA-196b-5p in Hepatocellular Carcinoma and its Potential Molecular Mechanism
Cited by: 11
Author(s): Lu Zhang, Bin Luo, Yi‐Wu Dang, Rong‐Quan He, Zhigang Peng, Gang Chen, Zhaoyong Feng
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0030781

Circadian Rhythms of Fetal Liver Transcription Persist in the Absence of Canonical Circadian Clock Gene Expression Rhythms In Vivo
Cited by: 8
Author(s): Chengwei Li, Shuang Yu, Xiaoling Zhong, Jianguo Wu, Xiaodong Li
Software Mentions: 1
Published: over 14 years ago

10.1186/1756-0500-4-78

Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2)
Cited by: 22
Author(s): Richard A. Lewis, Sanjay Shahi, Emma Laing, Giselda Bucca, Georgios Efthimiou, Michael E. Bushell, Colin P. Smith
Software Mentions: 1
Published: over 15 years ago

10.1186/1756-0500-7-148

Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays
Cited by: 0
Author(s): Liliana Sofia Mendonça Cardoso, Cláudia Elvas Suissas, Mário Ramirez, Marília Antunes, Francisco Pinto
Software Mentions: 1
Published: over 12 years ago

10.1186/1756-0500-5-401

Critical COPD respiratory illness is linked to increased transcriptomic activity of neutrophil proteases genes
Cited by: 33
Author(s): Raquel Almansa, Lorenzo Socías, Monica Sanchez-Garcia, Ignacio Martín‐Loeches, Milagros Del Olmo, David Andaluz‐Ojeda, Felipe Bobillo, Lucía Rico, Agueda Herrero, Vicente Roig, C Alicia San-Jose, Sara Rosich, Julia Barbado, Carlos Disdier, Raúl Ortíz de Lejarazu, Maria C Gallegos, Victoria Fernández, Jesús F. Bermejo-Martín
Software Mentions: 1
Published: about 14 years ago

10.7150/jca.34693

Distinct Roles of VEGFA and ANGPT2 in Lung Adenocarcinoma and Squamous Cell Carcinoma
Cited by: 20
Author(s): Shuang Qin, Ming Yi, Dechao Jiao, An‐Ping Li, Zeyu Wu
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2105-8-233

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data
Cited by: 46
Author(s): Miika J. Ahdesmäki, Harri Lähdesmäki, Andrew Y. Gracey, llya Shmulevich, Olli Yli‐Harja
Software Mentions: 1
Published: over 19 years ago

10.1186/s12859-020-03868-w

DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization
Cited by: 12
Author(s): Jin-Xing Liu, Mingming Gao, Zhen Cui, Ying-Lian Gao, Feng Li
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-021-04213-5

Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria
Cited by: 5
Author(s): Ian Leifer, Mishael Sánchez-Pérez, Cecilia Ishida, Hernán A. Makse
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.13023

Reduced angiogenic gene expression in morbillivirus‐triggered oncolysis in a translational model for histiocytic sarcoma
Cited by: 24
Author(s): Vanessa Maria Pfankuche, Ingo Spitzbarth, Stefanie Lapp, Reiner Ulrich, Ulrich Deschl, Arno Kalkuhl, Wolfgang Baumgärtner, Christina Puff
Software Mentions: 1
Published: almost 10 years ago

10.1186/1756-0500-3-16

Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
Cited by: 2
Author(s): Michael Gruenberger, Rudi Alberts, Damian Smedley, Morris A. Swertz, Paul N. Schofield, Klaus Schughart
Software Mentions: 1
Published: over 16 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: about 11 years ago

10.1371/journal.pone.0053391

Characterization of the Humoral Immune Response during Staphylococcus aureus Bacteremia and Global Gene Expression by Staphylococcus aureus in Human Blood
Cited by: 69
Author(s): P. Martijn den Reijer, Nicole Lemmens-den Toom, Samantha Kant, Susan V. Snijders, Hélène Boelens, Mehri Tavakol, Nelianne J. Verkaik, Alex van Belkum, Henri A. Verbrugh, Willem J. B. van Wamel
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0093175

Renal Tissue Thawed for 30 Minutes Is Still Suitable for Gene Expression Analysis
Cited by: 5
Author(s): Yi Ma, Xiaonan Kang, Weijun Ding, Haozheng Yang, Ye Wang, Jin Zeng, Yiran Huang, Hongyue Dai
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0152997

Overexpression and Biological Function of Ubiquitin-Specific Protease 42 in Gastric Cancer
Cited by: 19
Author(s): Kezuo Hou, Zhihua Zhu, Yong Wang, Chunhui Zhang, Shanshan Yu, Qingqing Zhu, Bo Yan
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2466-13-63

Altered microRNA expression profile during epithelial wound repair in bronchial epithelial cells
Cited by: 15
Author(s): Aleksandra Szczepankiewicz, Peter M. Lackie, John W. Holloway
Software Mentions: 1
Published: almost 13 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 14 years ago

10.1186/1471-244X-7-46

Inflammation-related genes up-regulated in schizophrenia brains
Cited by: 245
Author(s): Peter Saetre, Lina Emilsson, Elin Axelsson, Johan Kreuger, Eva Lindholm, Elena Jazin
Software Mentions: 1
Published: about 19 years ago

10.1186/1753-6561-5-S4-S4

Jejunal gene expression patterns correlate with severity of systemic infection in chicken
Cited by: 4
Author(s): Dirkjan Schokker, M.A. Smits, Johanna M.J. Rebel
Software Mentions: 1
Published: over 15 years ago

10.1111/jcmm.13051

Acquired TET 2 mutation in one patient with familial platelet disorder with predisposition to AML led to the development of pre‐leukaemic clone resulting in T2‐ ALL and AML ‐M0
Cited by: 10
Author(s): Vladimir T. Manchev, Hind Bouzid, Iléana Antony-Debré, Betty Leite, Guillaume Meurice, Nathalie Droin, Thomas Prébet, Régis Costello, William Vainchenker, Isabelle Plo, M’Boyba Diop, Elizabeth Macintyre, Vahid Asnafi, Rémi Favier, Véronique Baccini, Hana Raslová
Software Mentions: 1
Published: almost 10 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: almost 9 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 17 years ago

10.1186/1471-2229-10-77

Large impact of the apoplast on somatic embryogenesis in Cyclamen persicum offers possibilities for improved developmental control in vitro
Cited by: 30
Author(s): Claudia Hoenemann, Sandra Richardt, Katja Krüger, Andreas Zimmer, Annette Hohe, Stefan A. Rensing
Software Mentions: 1
Published: over 16 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: almost 15 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 15 years ago

10.1186/1471-2229-8-76

Articulation of three core metabolic processes in Arabidopsis: Fatty acid biosynthesis, leucine catabolism and starch metabolism
Cited by: 70
Author(s): Wieslawa I. Mentzen, Peng Jisheng, Nick Ransom, Basil J. Nikolau, Eve Syrkin Wurtele
Software Mentions: 1
Published: over 18 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 16 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: almost 21 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 13 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 10 years ago

10.1186/1471-2229-12-74

Effects of yeast trehalose-6-phosphate synthase 1 on gene expression and carbohydrate contents of potato leaves under drought stress conditions
Cited by: 57
Author(s): Mihály Kondrák, Ferenc Marincs, Ferenc Antal, Zsófia Juhász, Zsófia Bánfalvi
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0111168

The Porphyromonas gingivalis Ferric Uptake Regulator Orthologue Binds Hemin and Regulates Hemin-Responsive Biofilm Development
Cited by: 14
Author(s): Catherine A. Butler, Stuart G. Dashper, Lianyi Zhang, Christine A. Seers, Helen Mitchell, Deanne V. Catmull, Michelle D. Glew, Jacqueline E. Heath, Yan Tan, Hasnah Begum Said Ghulam Khan, Eric C. Reynolds
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0013069

Hfq Is a Global Regulator That Controls the Pathogenicity of Staphylococcus aureus
Cited by: 58
Author(s): Yu Liu, Na Wu, Jing Dong, Yaping Gao, Xin Zhang, Chunhua Mu, Ningsheng Shao, Guangxiao Yang
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2229-7-56

Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis
Cited by: 151
Author(s): Xiaoping Tan, Blake C. Meyers, Alexander Kozik, Marilyn A. L. West, Michèle Morgante, Dina A. St. Clair, Andrew F. Bent, Richard W. Michelmore
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2229-9-19

TRUNCATULIX - a data warehouse for the legume community
Cited by: 11
Author(s): Kolja Henckel, Kai J. Runte, Thomas Bekel, Michael Dondrup, Tobias Jakobi, H. Küster, Alexander Goesmann
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0131335

Alkbh8 Regulates Selenocysteine-Protein Expression to Protect against Reactive Oxygen Species Damage
Cited by: 64
Author(s): Lauren Endres, Ulrike Begley, Ryan R. Clark, Cheng Gu, Agnieszka Dziergowska, Andrzej Małkiewicz, J. Andrés Melendez, Peter C. Dedon, Thomas J. Begley
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0036776

MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer
Cited by: 9
Author(s): Akhilesh Kumar Bajpai, Sravanthi Davuluri, Darshan S. Chandrashekar, Ilakya Selvarajan, Mahalakshmi Dinakaran, Kshitish K. Acharya
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-12-97

Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms
Cited by: 1
Author(s): Andrew Timothy Milnthorpe, Mikhail Soloviev
Software Mentions: 1
Published: over 15 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962